data_6VHB
#
_entry.id 6VHB
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.387
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 6VHB pdb_00006vhb 10.2210/pdb6vhb/pdb
WWPDB D_1000246394 ? ?
EMDB EMD-21202 ? ?
#
loop_
_pdbx_audit_revision_history.ordinal
_pdbx_audit_revision_history.data_content_type
_pdbx_audit_revision_history.major_revision
_pdbx_audit_revision_history.minor_revision
_pdbx_audit_revision_history.revision_date
1 'Structure model' 1 0 2020-02-19
2 'Structure model' 1 1 2020-04-22
3 'Structure model' 1 2 2024-03-06
#
_pdbx_audit_revision_details.ordinal 1
_pdbx_audit_revision_details.revision_ordinal 1
_pdbx_audit_revision_details.data_content_type 'Structure model'
_pdbx_audit_revision_details.provider repository
_pdbx_audit_revision_details.type 'Initial release'
_pdbx_audit_revision_details.description ?
_pdbx_audit_revision_details.details ?
#
loop_
_pdbx_audit_revision_group.ordinal
_pdbx_audit_revision_group.revision_ordinal
_pdbx_audit_revision_group.data_content_type
_pdbx_audit_revision_group.group
1 2 'Structure model' 'Database references'
2 3 'Structure model' 'Data collection'
3 3 'Structure model' 'Database references'
4 3 'Structure model' 'Derived calculations'
5 3 'Structure model' 'Refinement description'
#
loop_
_pdbx_audit_revision_category.ordinal
_pdbx_audit_revision_category.revision_ordinal
_pdbx_audit_revision_category.data_content_type
_pdbx_audit_revision_category.category
1 2 'Structure model' citation
2 3 'Structure model' chem_comp_atom
3 3 'Structure model' chem_comp_bond
4 3 'Structure model' database_2
5 3 'Structure model' em_3d_fitting_list
6 3 'Structure model' pdbx_initial_refinement_model
7 3 'Structure model' pdbx_struct_conn_angle
8 3 'Structure model' struct_conn
#
loop_
_pdbx_audit_revision_item.ordinal
_pdbx_audit_revision_item.revision_ordinal
_pdbx_audit_revision_item.data_content_type
_pdbx_audit_revision_item.item
1 2 'Structure model' '_citation.journal_volume'
2 2 'Structure model' '_citation.page_first'
3 3 'Structure model' '_database_2.pdbx_DOI'
4 3 'Structure model' '_database_2.pdbx_database_accession'
5 3 'Structure model' '_em_3d_fitting_list.accession_code'
6 3 'Structure model' '_em_3d_fitting_list.initial_refinement_model_id'
7 3 'Structure model' '_em_3d_fitting_list.source_name'
8 3 'Structure model' '_em_3d_fitting_list.type'
9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id'
10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id'
11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id'
12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id'
13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id'
14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id'
15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id'
16 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id'
17 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id'
18 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id'
19 3 'Structure model' '_pdbx_struct_conn_angle.value'
20 3 'Structure model' '_struct_conn.pdbx_dist_value'
21 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id'
22 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id'
23 3 'Structure model' '_struct_conn.ptnr1_label_asym_id'
24 3 'Structure model' '_struct_conn.ptnr1_label_atom_id'
25 3 'Structure model' '_struct_conn.ptnr1_label_comp_id'
26 3 'Structure model' '_struct_conn.ptnr1_label_seq_id'
27 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id'
28 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id'
29 3 'Structure model' '_struct_conn.ptnr2_label_asym_id'
30 3 'Structure model' '_struct_conn.ptnr2_label_atom_id'
31 3 'Structure model' '_struct_conn.ptnr2_label_comp_id'
32 3 'Structure model' '_struct_conn.ptnr2_symmetry'
#
_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.entry_id 6VHB
_pdbx_database_status.recvd_initial_deposition_date 2020-01-09
_pdbx_database_status.SG_entry N
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.status_code_nmr_data ?
_pdbx_database_status.methods_development_category ?
_pdbx_database_status.pdb_format_compatible Y
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.details
_pdbx_database_related.db_id
_pdbx_database_related.content_type
PDB 'Original structure' 6cli unspecified
EMDB '1.4A low-dose structure of GSNQNNF determined from initial phases generated using radiation damage' EMD-21202
'associated EM volume'
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
_audit_author.identifier_ORCID
'Martynowycz, M.W.' 1 0000-0003-0055-230X
'Hattne, J.' 2 0000-0002-8936-0912
'Gonen, T.' 3 0000-0002-9254-4069
#
_citation.abstract ?
_citation.abstract_id_CAS ?
_citation.book_id_ISBN ?
_citation.book_publisher ?
_citation.book_publisher_city ?
_citation.book_title ?
_citation.coordinate_linkage ?
_citation.country UK
_citation.database_id_Medline ?
_citation.details ?
_citation.id primary
_citation.journal_abbrev Structure
_citation.journal_id_ASTM STRUE6
_citation.journal_id_CSD 2005
_citation.journal_id_ISSN 0969-2126
_citation.journal_full ?
_citation.journal_issue ?
_citation.journal_volume 28
_citation.language ?
_citation.page_first 458
_citation.page_last ?
_citation.title 'Experimental Phasing of MicroED Data Using Radiation Damage.'
_citation.year 2020
_citation.database_id_CSD ?
_citation.pdbx_database_id_DOI 10.1016/j.str.2020.01.008
_citation.pdbx_database_id_PubMed 32023481
_citation.unpublished_flag ?
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
_citation_author.identifier_ORCID
primary 'Martynowycz, M.W.' 1 ?
primary 'Hattne, J.' 2 ?
primary 'Gonen, T.' 3 ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer syn GSNQNNF 779.756 1 ? ? ? ?
2 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ?
3 non-polymer syn 'ACETATE ION' 59.044 1 ? ? ? ?
4 water nat water 18.015 1 ? ? ? ?
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code GSNQNNF
_entity_poly.pdbx_seq_one_letter_code_can GSNQNNF
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
loop_
_pdbx_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_entity_nonpoly.comp_id
2 'ZINC ION' ZN
3 'ACETATE ION' ACT
4 water HOH
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 GLY n
1 2 SER n
1 3 ASN n
1 4 GLN n
1 5 ASN n
1 6 ASN n
1 7 PHE n
#
_pdbx_entity_src_syn.entity_id 1
_pdbx_entity_src_syn.pdbx_src_id 1
_pdbx_entity_src_syn.pdbx_alt_source_flag sample
_pdbx_entity_src_syn.pdbx_beg_seq_num 1
_pdbx_entity_src_syn.pdbx_end_seq_num 7
_pdbx_entity_src_syn.organism_scientific 'synthetic construct'
_pdbx_entity_src_syn.organism_common_name ?
_pdbx_entity_src_syn.ncbi_taxonomy_id 32630
_pdbx_entity_src_syn.details ?
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
ACT non-polymer . 'ACETATE ION' ? 'C2 H3 O2 -1' 59.044
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118
GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144
GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067
HOH non-polymer . WATER ? 'H2 O' 18.015
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409
#
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_seq_num
_pdbx_poly_seq_scheme.pdb_seq_num
_pdbx_poly_seq_scheme.auth_seq_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
_pdbx_poly_seq_scheme.hetero
A 1 1 GLY 1 1 1 GLY GLY A . n
A 1 2 SER 2 2 2 SER SER A . n
A 1 3 ASN 3 3 3 ASN ASN A . n
A 1 4 GLN 4 4 4 GLN GLN A . n
A 1 5 ASN 5 5 5 ASN ASN A . n
A 1 6 ASN 6 6 6 ASN ASN A . n
A 1 7 PHE 7 7 7 PHE PHE A . n
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 ZN 1 101 0 ZN ZN A .
C 3 ACT 1 102 0 ACT ACT A .
D 4 HOH 1 201 1 HOH HOH A .
#
loop_
_software.citation_id
_software.classification
_software.compiler_name
_software.compiler_version
_software.contact_author
_software.contact_author_email
_software.date
_software.description
_software.dependencies
_software.hardware
_software.language
_software.location
_software.mods
_software.name
_software.os
_software.os_version
_software.type
_software.version
_software.pdbx_ordinal
? refinement ? ? ? ? ? ? ? ? ? ? ? SHELX ? ? ? .
1
? 'data reduction' ? ? 'Wolfgang Kabsch' Wolfgang.Kabsch@mpimf-heidelberg.mpg.de ? ? ? ? ?
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ ? XDS ? ? package . 2
? 'data scaling' ? ? 'Wolfgang Kabsch' ? ? ? ? ? ?
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? XSCALE ? ? package . 3
? 'data extraction' ? ? PDB deposit@deposit.rcsb.org 'Apr. 1, 2019' ? ? ? C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/ ? PDB_EXTRACT ? ? package 3.25 4
#
_cell.angle_alpha 83.600
_cell.angle_alpha_esd ?
_cell.angle_beta 84.980
_cell.angle_beta_esd ?
_cell.angle_gamma 83.310
_cell.angle_gamma_esd ?
_cell.entry_id 6VHB
_cell.details ?
_cell.formula_units_Z ?
_cell.length_a 4.880
_cell.length_a_esd ?
_cell.length_b 14.170
_cell.length_b_esd ?
_cell.length_c 17.620
_cell.length_c_esd ?
_cell.volume ?
_cell.volume_esd ?
_cell.Z_PDB 1
_cell.reciprocal_angle_alpha ?
_cell.reciprocal_angle_beta ?
_cell.reciprocal_angle_gamma ?
_cell.reciprocal_angle_alpha_esd ?
_cell.reciprocal_angle_beta_esd ?
_cell.reciprocal_angle_gamma_esd ?
_cell.reciprocal_length_a ?
_cell.reciprocal_length_b ?
_cell.reciprocal_length_c ?
_cell.reciprocal_length_a_esd ?
_cell.reciprocal_length_b_esd ?
_cell.reciprocal_length_c_esd ?
_cell.pdbx_unique_axis ?
#
_symmetry.entry_id 6VHB
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 1
_symmetry.space_group_name_Hall ?
_symmetry.space_group_name_H-M 'P 1'
_symmetry.pdbx_full_space_group_name_H-M ?
#
_exptl.absorpt_coefficient_mu ?
_exptl.absorpt_correction_T_max ?
_exptl.absorpt_correction_T_min ?
_exptl.absorpt_correction_type ?
_exptl.absorpt_process_details ?
_exptl.entry_id 6VHB
_exptl.crystals_number ?
_exptl.details ?
_exptl.method 'ELECTRON CRYSTALLOGRAPHY'
_exptl.method_details ?
#
_reflns.B_iso_Wilson_estimate 8.452
_reflns.entry_id 6VHB
_reflns.data_reduction_details ?
_reflns.data_reduction_method ?
_reflns.d_resolution_high 1.400
_reflns.d_resolution_low ?
_reflns.details ?
_reflns.limit_h_max ?
_reflns.limit_h_min ?
_reflns.limit_k_max ?
_reflns.limit_k_min ?
_reflns.limit_l_max ?
_reflns.limit_l_min ?
_reflns.number_all ?
_reflns.number_obs 713
_reflns.observed_criterion ?
_reflns.observed_criterion_F_max ?
_reflns.observed_criterion_F_min ?
_reflns.observed_criterion_I_max ?
_reflns.observed_criterion_I_min ?
_reflns.observed_criterion_sigma_F ?
_reflns.observed_criterion_sigma_I ?
_reflns.percent_possible_obs 77.200
_reflns.R_free_details ?
_reflns.Rmerge_F_all ?
_reflns.Rmerge_F_obs ?
_reflns.Friedel_coverage ?
_reflns.number_gt ?
_reflns.threshold_expression ?
_reflns.pdbx_redundancy 8.452
_reflns.pdbx_Rmerge_I_obs 0.208
_reflns.pdbx_Rmerge_I_all ?
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_av_sigmaI ?
_reflns.pdbx_netI_over_sigmaI 8.500
_reflns.pdbx_res_netI_over_av_sigmaI_2 ?
_reflns.pdbx_res_netI_over_sigmaI_2 ?
_reflns.pdbx_chi_squared 0.898
_reflns.pdbx_scaling_rejects 3
_reflns.pdbx_d_res_high_opt ?
_reflns.pdbx_d_res_low_opt ?
_reflns.pdbx_d_res_opt_method ?
_reflns.phase_calculation_details ?
_reflns.pdbx_Rrim_I_all 0.219
_reflns.pdbx_Rpim_I_all ?
_reflns.pdbx_d_opt ?
_reflns.pdbx_number_measured_all 6026
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
_reflns.pdbx_CC_half 0.973
_reflns.pdbx_CC_star ?
_reflns.pdbx_R_split ?
#
loop_
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.meanI_over_sigI_all
_reflns_shell.meanI_over_sigI_obs
_reflns_shell.number_measured_all
_reflns_shell.number_measured_obs
_reflns_shell.number_possible
_reflns_shell.number_unique_all
_reflns_shell.number_unique_obs
_reflns_shell.percent_possible_all
_reflns_shell.percent_possible_obs
_reflns_shell.Rmerge_F_all
_reflns_shell.Rmerge_F_obs
_reflns_shell.Rmerge_I_all
_reflns_shell.Rmerge_I_obs
_reflns_shell.meanI_over_sigI_gt
_reflns_shell.meanI_over_uI_all
_reflns_shell.meanI_over_uI_gt
_reflns_shell.number_measured_gt
_reflns_shell.number_unique_gt
_reflns_shell.percent_possible_gt
_reflns_shell.Rmerge_F_gt
_reflns_shell.Rmerge_I_gt
_reflns_shell.pdbx_redundancy
_reflns_shell.pdbx_Rsym_value
_reflns_shell.pdbx_chi_squared
_reflns_shell.pdbx_netI_over_sigmaI_all
_reflns_shell.pdbx_netI_over_sigmaI_obs
_reflns_shell.pdbx_Rrim_I_all
_reflns_shell.pdbx_Rpim_I_all
_reflns_shell.pdbx_rejects
_reflns_shell.pdbx_ordinal
_reflns_shell.pdbx_diffrn_id
_reflns_shell.pdbx_CC_half
_reflns_shell.pdbx_CC_star
_reflns_shell.pdbx_R_split
1.400 1.510 ? 6.610 ? 1308 195 ? 153 78.500 ? ? ? ? 0.262 ? ? ? ? ? ? ? ? 8.549 ? ? ? ? 0.278 ? ? 1 1 0.940 ? ?
1.510 1.660 ? 7.690 ? 1230 183 ? 143 78.100 ? ? ? ? 0.225 ? ? ? ? ? ? ? ? 8.601 ? ? ? ? 0.238 ? ? 2 1 0.965 ? ?
1.660 1.850 ? 7.680 ? 754 142 ? 105 73.900 ? ? ? ? 0.227 ? ? ? ? ? ? ? ? 7.181 ? ? ? ? 0.242 ? ? 3 1 0.955 ? ?
1.850 2.140 ? 9.370 ? 958 146 ? 114 78.100 ? ? ? ? 0.195 ? ? ? ? ? ? ? ? 8.404 ? ? ? ? 0.206 ? ? 4 1 0.982 ? ?
2.140 2.620 ? 10.250 ? 927 125 ? 97 77.600 ? ? ? ? 0.200 ? ? ? ? ? ? ? ? 9.557 ? ? ? ? 0.210 ? ? 5 1 0.968 ? ?
2.620 3.700 ? 10.310 ? 501 83 ? 63 75.900 ? ? ? ? 0.195 ? ? ? ? ? ? ? ? 7.952 ? ? ? ? 0.205 ? ? 6 1 0.955 ? ?
3.700 ? ? 11.360 ? 348 50 ? 38 76.000 ? ? ? ? 0.195 ? ? ? ? ? ? ? ? 9.158 ? ? ? ? 0.205 ? ? 7 1 0.964 ? ?
#
_refine.aniso_B[1][1] ?
_refine.aniso_B[1][2] ?
_refine.aniso_B[1][3] ?
_refine.aniso_B[2][2] ?
_refine.aniso_B[2][3] ?
_refine.aniso_B[3][3] ?
_refine.B_iso_max 9.960
_refine.B_iso_mean 2.5608
_refine.B_iso_min 0.080
_refine.correlation_coeff_Fo_to_Fc ?
_refine.correlation_coeff_Fo_to_Fc_free ?
_refine.details ?
_refine.diff_density_max ?
_refine.diff_density_max_esd ?
_refine.diff_density_min ?
_refine.diff_density_min_esd ?
_refine.diff_density_rms ?
_refine.diff_density_rms_esd ?
_refine.entry_id 6VHB
_refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY'
_refine.ls_abs_structure_details ?
_refine.ls_abs_structure_Flack ?
_refine.ls_abs_structure_Flack_esd ?
_refine.ls_abs_structure_Rogers ?
_refine.ls_abs_structure_Rogers_esd ?
_refine.ls_d_res_high 1.4
_refine.ls_d_res_low 14.0
_refine.ls_extinction_coef ?
_refine.ls_extinction_coef_esd ?
_refine.ls_extinction_expression ?
_refine.ls_extinction_method ?
_refine.ls_goodness_of_fit_all ?
_refine.ls_goodness_of_fit_all_esd ?
_refine.ls_goodness_of_fit_obs ?
_refine.ls_goodness_of_fit_obs_esd ?
_refine.ls_hydrogen_treatment ?
_refine.ls_matrix_type ?
_refine.ls_number_constraints ?
_refine.ls_number_parameters ?
_refine.ls_number_reflns_all ?
_refine.ls_number_reflns_obs 713
_refine.ls_number_reflns_R_free ?
_refine.ls_number_reflns_R_work ?
_refine.ls_number_restraints ?
_refine.ls_percent_reflns_obs 77.2
_refine.ls_percent_reflns_R_free ?
_refine.ls_R_factor_all ?
_refine.ls_R_factor_obs ?
_refine.ls_R_factor_R_free 0.289
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_R_factor_R_work 0.222
_refine.ls_R_Fsqd_factor_obs ?
_refine.ls_R_I_factor_obs ?
_refine.ls_redundancy_reflns_all ?
_refine.ls_redundancy_reflns_obs ?
_refine.ls_restrained_S_all ?
_refine.ls_restrained_S_obs ?
_refine.ls_shift_over_esd_max ?
_refine.ls_shift_over_esd_mean ?
_refine.ls_structure_factor_coef ?
_refine.ls_weighting_details ?
_refine.ls_weighting_scheme ?
_refine.ls_wR_factor_all ?
_refine.ls_wR_factor_obs ?
_refine.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.occupancy_max ?
_refine.occupancy_min ?
_refine.solvent_model_details ?
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.pdbx_R_complete ?
_refine.ls_R_factor_gt ?
_refine.ls_goodness_of_fit_gt ?
_refine.ls_goodness_of_fit_ref ?
_refine.ls_shift_over_su_max ?
_refine.ls_shift_over_su_max_lt ?
_refine.ls_shift_over_su_mean ?
_refine.ls_shift_over_su_mean_lt ?
_refine.pdbx_ls_sigma_I ?
_refine.pdbx_ls_sigma_F ?
_refine.pdbx_ls_sigma_Fsqd ?
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_isotropic_thermal_model ?
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.pdbx_method_to_determine_struct ?
_refine.pdbx_starting_model ?
_refine.pdbx_stereochemistry_target_values ?
_refine.pdbx_R_Free_selection_details 'Rcomplete random'
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_overall_ESU_R ?
_refine.pdbx_overall_ESU_R_Free ?
_refine.pdbx_solvent_vdw_probe_radii ?
_refine.pdbx_solvent_ion_probe_radii ?
_refine.pdbx_solvent_shrinkage_radii ?
_refine.pdbx_real_space_R ?
_refine.pdbx_density_correlation ?
_refine.pdbx_pd_number_of_powder_patterns ?
_refine.pdbx_pd_number_of_points ?
_refine.pdbx_pd_meas_number_of_points ?
_refine.pdbx_pd_proc_ls_prof_R_factor ?
_refine.pdbx_pd_proc_ls_prof_wR_factor ?
_refine.pdbx_pd_Marquardt_correlation_coeff ?
_refine.pdbx_pd_Fsqrd_R_factor ?
_refine.pdbx_pd_ls_matrix_band_width ?
_refine.pdbx_overall_phase_error ?
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_TLS_residual_ADP_flag ?
_refine.pdbx_diffrn_id 1
_refine.overall_SU_B ?
_refine.overall_SU_ML ?
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_refine.overall_FOM_free_R_set ?
_refine.overall_FOM_work_R_set ?
_refine.pdbx_average_fsc_overall ?
_refine.pdbx_average_fsc_work ?
_refine.pdbx_average_fsc_free ?
#
_struct.entry_id 6VHB
_struct.title
'1.4A low-dose structure of GSNQNNF determined from initial phases generated using radiation damage'
_struct.pdbx_model_details ?
_struct.pdbx_formula_weight ?
_struct.pdbx_formula_weight_method ?
_struct.pdbx_model_type_details ?
_struct.pdbx_CASP_flag N
#
_struct_keywords.entry_id 6VHB
_struct_keywords.text 'MicroED, damage, phasing, RIP, protein fibril'
_struct_keywords.pdbx_keywords 'PROTEIN FIBRIL'
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
C N N 3 ?
D N N 4 ?
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 6VHB
_struct_ref.pdbx_db_accession 6VHB
_struct_ref.pdbx_db_isoform ?
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_align_begin 1
#
_struct_ref_seq.align_id 1
_struct_ref_seq.ref_id 1
_struct_ref_seq.pdbx_PDB_id_code 6VHB
_struct_ref_seq.pdbx_strand_id A
_struct_ref_seq.seq_align_beg 1
_struct_ref_seq.pdbx_seq_align_beg_ins_code ?
_struct_ref_seq.seq_align_end 7
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession 6VHB
_struct_ref_seq.db_align_beg 1
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 7
_struct_ref_seq.pdbx_db_align_end_ins_code ?
_struct_ref_seq.pdbx_auth_seq_align_beg 1
_struct_ref_seq.pdbx_auth_seq_align_end 7
#
_pdbx_struct_assembly.id 1
_pdbx_struct_assembly.details author_defined_assembly
_pdbx_struct_assembly.method_details ?
_pdbx_struct_assembly.oligomeric_details monomeric
_pdbx_struct_assembly.oligomeric_count 1
#
_pdbx_struct_assembly_gen.assembly_id 1
_pdbx_struct_assembly_gen.oper_expression 1
_pdbx_struct_assembly_gen.asym_id_list A,B,C,D
#
_pdbx_struct_assembly_auth_evidence.id 1
_pdbx_struct_assembly_auth_evidence.assembly_id 1
_pdbx_struct_assembly_auth_evidence.experimental_support microscopy
_pdbx_struct_assembly_auth_evidence.details ?
#
_pdbx_struct_oper_list.id 1
_pdbx_struct_oper_list.type 'identity operation'
_pdbx_struct_oper_list.name 1_555
_pdbx_struct_oper_list.symmetry_operation x,y,z
_pdbx_struct_oper_list.matrix[1][1] 1.0000000000
_pdbx_struct_oper_list.matrix[1][2] 0.0000000000
_pdbx_struct_oper_list.matrix[1][3] 0.0000000000
_pdbx_struct_oper_list.vector[1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][1] 0.0000000000
_pdbx_struct_oper_list.matrix[2][2] 1.0000000000
_pdbx_struct_oper_list.matrix[2][3] 0.0000000000
_pdbx_struct_oper_list.vector[2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][1] 0.0000000000
_pdbx_struct_oper_list.matrix[3][2] 0.0000000000
_pdbx_struct_oper_list.matrix[3][3] 1.0000000000
_pdbx_struct_oper_list.vector[3] 0.0000000000
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
_struct_conn.pdbx_role
metalc1 metalc ? ? A GLY 1 N ? ? ? 1_555 B ZN . ZN ? ? A GLY 1 A ZN 101 1_555 ? ? ? ? ? ? ? 1.981 ? ?
metalc2 metalc ? ? A GLY 1 O ? ? ? 1_555 B ZN . ZN ? ? A GLY 1 A ZN 101 1_555 ? ? ? ? ? ? ? 1.855 ? ?
metalc3 metalc ? ? A PHE 7 O ? ? ? 1_555 B ZN . ZN ? ? A PHE 7 A ZN 101 1_644 ? ? ? ? ? ? ? 2.086 ? ?
metalc4 metalc ? ? B ZN . ZN ? ? ? 1_555 C ACT . O ? ? A ZN 101 A ACT 102 1_555 ? ? ? ? ? ? ? 2.049 ? ?
metalc5 metalc ? ? B ZN . ZN ? ? ? 1_555 C ACT . OXT ? ? A ZN 101 A ACT 102 1_655 ? ? ? ? ? ? ? 2.026 ? ?
#
_struct_conn_type.id metalc
_struct_conn_type.criteria ?
_struct_conn_type.reference ?
#
loop_
_pdbx_struct_conn_angle.id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_alt_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_auth_atom_id
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_PDB_ins_code
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_alt_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr2_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_atom_id
_pdbx_struct_conn_angle.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_PDB_ins_code
_pdbx_struct_conn_angle.ptnr2_symmetry
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_alt_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_atom_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_PDB_ins_code
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_pdbx_struct_conn_angle.value_esd
1 N ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 O ? A GLY 1 ? A GLY 1 ? 1_555 85.4 ?
2 N ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 O ? A PHE 7 ? A PHE 7 ? 1_555 115.0 ?
3 O ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 O ? A PHE 7 ? A PHE 7 ? 1_555 45.1 ?
4 N ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 O ? C ACT . ? A ACT 102 ? 1_555 146.1 ?
5 O ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 O ? C ACT . ? A ACT 102 ? 1_555 87.4 ?
6 O ? A PHE 7 ? A PHE 7 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 O ? C ACT . ? A ACT 102 ? 1_555 81.3 ?
7 N ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 OXT ? C ACT . ? A ACT 102 ? 1_655 115.7 ?
8 O ? A GLY 1 ? A GLY 1 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 OXT ? C ACT . ? A ACT 102 ? 1_655 97.3 ?
9 O ? A PHE 7 ? A PHE 7 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 OXT ? C ACT . ? A ACT 102 ? 1_655 54.5 ?
10 O ? C ACT . ? A ACT 102 ? 1_555 ZN ? B ZN . ? A ZN 101 ? 1_555 OXT ? C ACT . ? A ACT 102 ? 1_655 98.0 ?
#
loop_
_struct_site.id
_struct_site.pdbx_evidence_code
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_struct_site.pdbx_auth_ins_code
_struct_site.pdbx_num_residues
_struct_site.details
AC1 Software A ZN 101 ? 2 'binding site for residue ZN A 101'
AC2 Software A ACT 102 ? 2 'binding site for residue ACT A 102'
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 2 GLY A 1 ? GLY A 1 . ? 1_555 ?
2 AC1 2 ACT C . ? ACT A 102 . ? 1_555 ?
3 AC2 2 GLY A 1 ? GLY A 1 . ? 1_555 ?
4 AC2 2 ZN B . ? ZN A 101 . ? 1_555 ?
#
_pdbx_validate_rmsd_angle.id 1
_pdbx_validate_rmsd_angle.PDB_model_num 1
_pdbx_validate_rmsd_angle.auth_atom_id_1 CG
_pdbx_validate_rmsd_angle.auth_asym_id_1 A
_pdbx_validate_rmsd_angle.auth_comp_id_1 PHE
_pdbx_validate_rmsd_angle.auth_seq_id_1 7
_pdbx_validate_rmsd_angle.PDB_ins_code_1 ?
_pdbx_validate_rmsd_angle.label_alt_id_1 ?
_pdbx_validate_rmsd_angle.auth_atom_id_2 CD1
_pdbx_validate_rmsd_angle.auth_asym_id_2 A
_pdbx_validate_rmsd_angle.auth_comp_id_2 PHE
_pdbx_validate_rmsd_angle.auth_seq_id_2 7
_pdbx_validate_rmsd_angle.PDB_ins_code_2 ?
_pdbx_validate_rmsd_angle.label_alt_id_2 ?
_pdbx_validate_rmsd_angle.auth_atom_id_3 CE1
_pdbx_validate_rmsd_angle.auth_asym_id_3 A
_pdbx_validate_rmsd_angle.auth_comp_id_3 PHE
_pdbx_validate_rmsd_angle.auth_seq_id_3 7
_pdbx_validate_rmsd_angle.PDB_ins_code_3 ?
_pdbx_validate_rmsd_angle.label_alt_id_3 ?
_pdbx_validate_rmsd_angle.angle_value 127.67
_pdbx_validate_rmsd_angle.angle_target_value 120.80
_pdbx_validate_rmsd_angle.angle_deviation 6.87
_pdbx_validate_rmsd_angle.angle_standard_deviation 1.10
_pdbx_validate_rmsd_angle.linker_flag N
#
_pdbx_entry_details.entry_id 6VHB
_pdbx_entry_details.has_ligand_of_interest N
_pdbx_entry_details.compound_details ?
_pdbx_entry_details.source_details ?
_pdbx_entry_details.nonpolymer_details ?
_pdbx_entry_details.sequence_details ?
#
_em_3d_fitting.entry_id 6VHB
_em_3d_fitting.id 1
_em_3d_fitting.details ?
_em_3d_fitting.overall_b_value 2
_em_3d_fitting.ref_protocol OTHER
_em_3d_fitting.ref_space RECIPROCAL
_em_3d_fitting.target_criteria ?
_em_3d_fitting.method ?
#
_em_3d_fitting_list.3d_fitting_id 1
_em_3d_fitting_list.id 1
_em_3d_fitting_list.details ?
_em_3d_fitting_list.pdb_chain_id A
_em_3d_fitting_list.pdb_chain_residue_range 1-7
_em_3d_fitting_list.pdb_entry_id 6CLI
_em_3d_fitting_list.initial_refinement_model_id 1
_em_3d_fitting_list.chain_id ?
_em_3d_fitting_list.chain_residue_range ?
_em_3d_fitting_list.source_name PDB
_em_3d_fitting_list.type 'experimental model'
_em_3d_fitting_list.accession_code 6CLI
#
_em_3d_reconstruction.entry_id 6VHB
_em_3d_reconstruction.id 1
_em_3d_reconstruction.algorithm ?
_em_3d_reconstruction.details ?
_em_3d_reconstruction.refinement_type ?
_em_3d_reconstruction.image_processing_id 1
_em_3d_reconstruction.num_class_averages ?
_em_3d_reconstruction.num_particles ?
_em_3d_reconstruction.resolution 1.4
_em_3d_reconstruction.resolution_method 'DIFFRACTION PATTERN/LAYERLINES'
_em_3d_reconstruction.symmetry_type '3D CRYSTAL'
_em_3d_reconstruction.method ?
_em_3d_reconstruction.nominal_pixel_size ?
_em_3d_reconstruction.actual_pixel_size ?
_em_3d_reconstruction.magnification_calibration ?
#
_em_buffer.id 1
_em_buffer.details ?
_em_buffer.pH 6.0
_em_buffer.specimen_id 1
_em_buffer.name ?
#
_em_entity_assembly.id 1
_em_entity_assembly.parent_id 0
_em_entity_assembly.details ?
_em_entity_assembly.name 'Synthetic proto-filament'
_em_entity_assembly.source NATURAL
_em_entity_assembly.type COMPLEX
_em_entity_assembly.entity_id_list 1
_em_entity_assembly.synonym ?
_em_entity_assembly.oligomeric_details ?
#
_em_image_scans.entry_id 6VHB
_em_image_scans.id 1
_em_image_scans.dimension_height 2048
_em_image_scans.dimension_width 2048
_em_image_scans.frames_per_image ?
_em_image_scans.image_recording_id 1
_em_image_scans.sampling_size 31.2
_em_image_scans.scanner_model ?
_em_image_scans.used_frames_per_image ?
_em_image_scans.citation_id ?
_em_image_scans.number_digital_images ?
_em_image_scans.od_range ?
_em_image_scans.quant_bit_size ?
_em_image_scans.details ?
#
_em_imaging.id 1
_em_imaging.entry_id 6VHB
_em_imaging.accelerating_voltage 200
_em_imaging.alignment_procedure ?
_em_imaging.c2_aperture_diameter 100
_em_imaging.calibrated_defocus_max ?
_em_imaging.calibrated_defocus_min ?
_em_imaging.calibrated_magnification ?
_em_imaging.cryogen NITROGEN
_em_imaging.details ?
_em_imaging.electron_source 'FIELD EMISSION GUN'
_em_imaging.illumination_mode 'FLOOD BEAM'
_em_imaging.microscope_model 'FEI TECNAI F20'
_em_imaging.mode DIFFRACTION
_em_imaging.nominal_cs ?
_em_imaging.nominal_defocus_max ?
_em_imaging.nominal_defocus_min ?
_em_imaging.nominal_magnification ?
_em_imaging.recording_temperature_maximum ?
_em_imaging.recording_temperature_minimum ?
_em_imaging.residual_tilt ?
_em_imaging.specimen_holder_model 'GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER'
_em_imaging.specimen_id 1
_em_imaging.citation_id ?
_em_imaging.date ?
_em_imaging.temperature ?
_em_imaging.tilt_angle_min ?
_em_imaging.tilt_angle_max ?
_em_imaging.astigmatism ?
_em_imaging.detector_distance ?
_em_imaging.electron_beam_tilt_params ?
_em_imaging.specimen_holder_type ?
#
_em_sample_support.id 1
_em_sample_support.specimen_id 1
_em_sample_support.details ?
_em_sample_support.grid_material COPPER
_em_sample_support.grid_mesh_size 300
_em_sample_support.grid_type 'Quantifoil R2/2'
_em_sample_support.method ?
_em_sample_support.film_material ?
#
_em_vitrification.id 1
_em_vitrification.specimen_id 1
_em_vitrification.chamber_temperature ?
_em_vitrification.cryogen_name ETHANE
_em_vitrification.details ?
_em_vitrification.humidity 30
_em_vitrification.instrument 'FEI VITROBOT MARK IV'
_em_vitrification.entry_id 6VHB
_em_vitrification.citation_id ?
_em_vitrification.method ?
_em_vitrification.temp ?
_em_vitrification.time_resolved_state ?
#
_em_experiment.entry_id 6VHB
_em_experiment.id 1
_em_experiment.aggregation_state '3D ARRAY'
_em_experiment.reconstruction_method CRYSTALLOGRAPHY
_em_experiment.entity_assembly_id 1
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_ordinal
ACT C C N N 1
ACT O O N N 2
ACT OXT O N N 3
ACT CH3 C N N 4
ACT H1 H N N 5
ACT H2 H N N 6
ACT H3 H N N 7
ASN N N N N 8
ASN CA C N S 9
ASN C C N N 10
ASN O O N N 11
ASN CB C N N 12
ASN CG C N N 13
ASN OD1 O N N 14
ASN ND2 N N N 15
ASN OXT O N N 16
ASN H H N N 17
ASN H2 H N N 18
ASN HA H N N 19
ASN HB2 H N N 20
ASN HB3 H N N 21
ASN HD21 H N N 22
ASN HD22 H N N 23
ASN HXT H N N 24
GLN N N N N 25
GLN CA C N S 26
GLN C C N N 27
GLN O O N N 28
GLN CB C N N 29
GLN CG C N N 30
GLN CD C N N 31
GLN OE1 O N N 32
GLN NE2 N N N 33
GLN OXT O N N 34
GLN H H N N 35
GLN H2 H N N 36
GLN HA H N N 37
GLN HB2 H N N 38
GLN HB3 H N N 39
GLN HG2 H N N 40
GLN HG3 H N N 41
GLN HE21 H N N 42
GLN HE22 H N N 43
GLN HXT H N N 44
GLY N N N N 45
GLY CA C N N 46
GLY C C N N 47
GLY O O N N 48
GLY OXT O N N 49
GLY H H N N 50
GLY H2 H N N 51
GLY HA2 H N N 52
GLY HA3 H N N 53
GLY HXT H N N 54
HOH O O N N 55
HOH H1 H N N 56
HOH H2 H N N 57
PHE N N N N 58
PHE CA C N S 59
PHE C C N N 60
PHE O O N N 61
PHE CB C N N 62
PHE CG C Y N 63
PHE CD1 C Y N 64
PHE CD2 C Y N 65
PHE CE1 C Y N 66
PHE CE2 C Y N 67
PHE CZ C Y N 68
PHE OXT O N N 69
PHE H H N N 70
PHE H2 H N N 71
PHE HA H N N 72
PHE HB2 H N N 73
PHE HB3 H N N 74
PHE HD1 H N N 75
PHE HD2 H N N 76
PHE HE1 H N N 77
PHE HE2 H N N 78
PHE HZ H N N 79
PHE HXT H N N 80
SER N N N N 81
SER CA C N S 82
SER C C N N 83
SER O O N N 84
SER CB C N N 85
SER OG O N N 86
SER OXT O N N 87
SER H H N N 88
SER H2 H N N 89
SER HA H N N 90
SER HB2 H N N 91
SER HB3 H N N 92
SER HG H N N 93
SER HXT H N N 94
ZN ZN ZN N N 95
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
ACT C O doub N N 1
ACT C OXT sing N N 2
ACT C CH3 sing N N 3
ACT CH3 H1 sing N N 4
ACT CH3 H2 sing N N 5
ACT CH3 H3 sing N N 6
ASN N CA sing N N 7
ASN N H sing N N 8
ASN N H2 sing N N 9
ASN CA C sing N N 10
ASN CA CB sing N N 11
ASN CA HA sing N N 12
ASN C O doub N N 13
ASN C OXT sing N N 14
ASN CB CG sing N N 15
ASN CB HB2 sing N N 16
ASN CB HB3 sing N N 17
ASN CG OD1 doub N N 18
ASN CG ND2 sing N N 19
ASN ND2 HD21 sing N N 20
ASN ND2 HD22 sing N N 21
ASN OXT HXT sing N N 22
GLN N CA sing N N 23
GLN N H sing N N 24
GLN N H2 sing N N 25
GLN CA C sing N N 26
GLN CA CB sing N N 27
GLN CA HA sing N N 28
GLN C O doub N N 29
GLN C OXT sing N N 30
GLN CB CG sing N N 31
GLN CB HB2 sing N N 32
GLN CB HB3 sing N N 33
GLN CG CD sing N N 34
GLN CG HG2 sing N N 35
GLN CG HG3 sing N N 36
GLN CD OE1 doub N N 37
GLN CD NE2 sing N N 38
GLN NE2 HE21 sing N N 39
GLN NE2 HE22 sing N N 40
GLN OXT HXT sing N N 41
GLY N CA sing N N 42
GLY N H sing N N 43
GLY N H2 sing N N 44
GLY CA C sing N N 45
GLY CA HA2 sing N N 46
GLY CA HA3 sing N N 47
GLY C O doub N N 48
GLY C OXT sing N N 49
GLY OXT HXT sing N N 50
HOH O H1 sing N N 51
HOH O H2 sing N N 52
PHE N CA sing N N 53
PHE N H sing N N 54
PHE N H2 sing N N 55
PHE CA C sing N N 56
PHE CA CB sing N N 57
PHE CA HA sing N N 58
PHE C O doub N N 59
PHE C OXT sing N N 60
PHE CB CG sing N N 61
PHE CB HB2 sing N N 62
PHE CB HB3 sing N N 63
PHE CG CD1 doub Y N 64
PHE CG CD2 sing Y N 65
PHE CD1 CE1 sing Y N 66
PHE CD1 HD1 sing N N 67
PHE CD2 CE2 doub Y N 68
PHE CD2 HD2 sing N N 69
PHE CE1 CZ doub Y N 70
PHE CE1 HE1 sing N N 71
PHE CE2 CZ sing Y N 72
PHE CE2 HE2 sing N N 73
PHE CZ HZ sing N N 74
PHE OXT HXT sing N N 75
SER N CA sing N N 76
SER N H sing N N 77
SER N H2 sing N N 78
SER CA C sing N N 79
SER CA CB sing N N 80
SER CA HA sing N N 81
SER C O doub N N 82
SER C OXT sing N N 83
SER CB OG sing N N 84
SER CB HB2 sing N N 85
SER CB HB3 sing N N 86
SER OG HG sing N N 87
SER OXT HXT sing N N 88
#
_em_3d_crystal_entity.id 1
_em_3d_crystal_entity.image_processing_id 1
_em_3d_crystal_entity.angle_alpha 83.60
_em_3d_crystal_entity.angle_beta 84.98
_em_3d_crystal_entity.angle_gamma 83.31
_em_3d_crystal_entity.length_a 4.880
_em_3d_crystal_entity.length_b 14.17
_em_3d_crystal_entity.length_c 17.62
_em_3d_crystal_entity.space_group_name 1
_em_3d_crystal_entity.space_group_num 1
#
loop_
_em_buffer_component.buffer_id
_em_buffer_component.id
_em_buffer_component.concentration
_em_buffer_component.concentration_units
_em_buffer_component.formula
_em_buffer_component.name
1 1 0.1 M C6H13NO4S MES
1 2 10 % C6H14O2 MPD
#
_em_ctf_correction.id 1
_em_ctf_correction.em_image_processing_id 1
_em_ctf_correction.type NONE
_em_ctf_correction.details ?
#
_em_diffraction.id 1
_em_diffraction.camera_length 730
_em_diffraction.imaging_id 1
_em_diffraction.tilt_angle_list ?
#
_em_diffraction_shell.id 1
_em_diffraction_shell.em_diffraction_stats_id 1
_em_diffraction_shell.fourier_space_coverage 77.2
_em_diffraction_shell.high_resolution 14
_em_diffraction_shell.low_resolution 1.4
_em_diffraction_shell.multiplicity 8.5
_em_diffraction_shell.num_structure_factors 713
_em_diffraction_shell.phase_residual 24
#
_em_diffraction_stats.id 1
_em_diffraction_stats.details
;Initial phases were obtained by taking the difference between the low-dose and damaged set, and locating the zinc atom to generate experimental phases.
;
_em_diffraction_stats.image_processing_id 1
_em_diffraction_stats.fourier_space_coverage 77.2
_em_diffraction_stats.high_resolution 1.4
_em_diffraction_stats.num_intensities_measured 6026
_em_diffraction_stats.num_structure_factors 713
_em_diffraction_stats.overall_phase_error 24
_em_diffraction_stats.overall_phase_residual 24
_em_diffraction_stats.phase_error_rejection_criteria 0.0
_em_diffraction_stats.r_merge 0.208
_em_diffraction_stats.r_sym 0.219
#
_em_entity_assembly_molwt.entity_assembly_id 1
_em_entity_assembly_molwt.id 1
_em_entity_assembly_molwt.experimental_flag NO
_em_entity_assembly_molwt.units MEGADALTONS
_em_entity_assembly_molwt.value 0.000899141
#
_em_entity_assembly_naturalsource.cell ?
_em_entity_assembly_naturalsource.cellular_location ?
_em_entity_assembly_naturalsource.entity_assembly_id 1
_em_entity_assembly_naturalsource.id 1
_em_entity_assembly_naturalsource.ncbi_tax_id 32630
_em_entity_assembly_naturalsource.organ ?
_em_entity_assembly_naturalsource.organelle ?
_em_entity_assembly_naturalsource.organism 'synthetic construct'
_em_entity_assembly_naturalsource.strain ?
_em_entity_assembly_naturalsource.tissue ?
#
_em_image_processing.id 1
_em_image_processing.image_recording_id 1
_em_image_processing.details 'Rolling shutter and binned by 2.'
#
_em_image_recording.id 1
_em_image_recording.imaging_id 1
_em_image_recording.avg_electron_dose_per_image 0.00588
_em_image_recording.average_exposure_time 2.1
_em_image_recording.details 'Images collected as movies.'
_em_image_recording.detector_mode ?
_em_image_recording.film_or_detector_model 'TVIPS TEMCAM-F416 (4k x 4k)'
_em_image_recording.num_diffraction_images 736
_em_image_recording.num_grids_imaged 1
_em_image_recording.num_real_images 736
#
loop_
_em_software.id
_em_software.category
_em_software.details
_em_software.name
_em_software.version
_em_software.image_processing_id
_em_software.fitting_id
_em_software.imaging_id
1 'IMAGE ACQUISITION' ? EM-Menu 4.0.9.75 ? ? 1
2 MASKING ? ? ? ? ? ?
3 'CTF CORRECTION' ? ? ? 1 ? ?
4 'LAYERLINE INDEXING' ? ? ? ? ? ?
5 'DIFFRACTION INDEXING' ? ? ? ? ? ?
6 'MODEL FITTING' ? ? ? ? 1 ?
7 OTHER ? ? ? ? ? ?
8 'MODEL REFINEMENT' ? ? ? ? 1 ?
9 'MOLECULAR REPLACEMENT' ? ? ? 1 ? ?
10 'LATTICE DISTORTION CORRECTION' ? ? ? 1 ? ?
11 'SYMMETRY DETERMINATION' ? ? ? 1 ? ?
12 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 ? ?
13 RECONSTRUCTION ? ? ? 1 ? ?
#
_em_specimen.id 1
_em_specimen.experiment_id 1
_em_specimen.concentration 10
_em_specimen.details 'Hanging drop.'
_em_specimen.embedding_applied NO
_em_specimen.shadowing_applied NO
_em_specimen.staining_applied NO
_em_specimen.vitrification_applied YES
#
_pdbx_initial_refinement_model.id 1
_pdbx_initial_refinement_model.type 'experimental model'
_pdbx_initial_refinement_model.source_name PDB
_pdbx_initial_refinement_model.accession_code 6CLI
#
_atom_sites.entry_id 6VHB
_atom_sites.Cartn_transf_matrix[1][1] ?
_atom_sites.Cartn_transf_matrix[1][2] ?
_atom_sites.Cartn_transf_matrix[1][3] ?
_atom_sites.Cartn_transf_matrix[2][1] ?
_atom_sites.Cartn_transf_matrix[2][2] ?
_atom_sites.Cartn_transf_matrix[2][3] ?
_atom_sites.Cartn_transf_matrix[3][1] ?
_atom_sites.Cartn_transf_matrix[3][2] ?
_atom_sites.Cartn_transf_matrix[3][3] ?
_atom_sites.Cartn_transf_vector[1] ?
_atom_sites.Cartn_transf_vector[2] ?
_atom_sites.Cartn_transf_vector[3] ?
_atom_sites.fract_transf_matrix[1][1] 0.204918
_atom_sites.fract_transf_matrix[1][2] -0.024036
_atom_sites.fract_transf_matrix[1][3] -0.015622
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.071055
_atom_sites.fract_transf_matrix[2][3] -0.007312
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 0.057273
_atom_sites.fract_transf_vector[1] 0.000000
_atom_sites.fract_transf_vector[2] 0.000000
_atom_sites.fract_transf_vector[3] 0.000000
_atom_sites.solution_primary ?
_atom_sites.solution_secondary ?
_atom_sites.solution_hydrogens ?
_atom_sites.special_details ?
#
loop_
_atom_type.symbol
C
N
O
ZN
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . GLY A 1 1 ? 3.399 30.601 19.375 1.00 0.93 ? 1 GLY A N 1
ATOM 2 C CA . GLY A 1 1 ? 3.623 30.787 17.936 1.00 2.92 ? 1 GLY A CA 1
ATOM 3 C C . GLY A 1 1 ? 2.760 29.752 17.177 1.00 2.30 ? 1 GLY A C 1
ATOM 4 O O . GLY A 1 1 ? 2.082 28.974 17.829 1.00 1.80 ? 1 GLY A O 1
ATOM 5 N N . SER A 1 2 ? 2.858 29.801 15.858 1.00 0.08 ? 2 SER A N 1
ATOM 6 C CA . SER A 1 2 ? 1.978 28.995 15.000 1.00 0.69 ? 2 SER A CA 1
ATOM 7 C C . SER A 1 2 ? 2.692 27.753 14.486 1.00 0.08 ? 2 SER A C 1
ATOM 8 O O . SER A 1 2 ? 3.941 27.738 14.345 1.00 5.90 ? 2 SER A O 1
ATOM 9 C CB . SER A 1 2 ? 1.496 29.908 13.854 1.00 0.08 ? 2 SER A CB 1
ATOM 10 O OG . SER A 1 2 ? 0.525 30.854 14.292 1.00 1.15 ? 2 SER A OG 1
ATOM 11 N N . ASN A 1 3 ? 2.001 26.639 14.227 1.00 3.22 ? 3 ASN A N 1
ATOM 12 C CA . ASN A 1 3 ? 2.564 25.333 13.879 1.00 0.71 ? 3 ASN A CA 1
ATOM 13 C C . ASN A 1 3 ? 1.886 24.766 12.635 1.00 5.01 ? 3 ASN A C 1
ATOM 14 O O . ASN A 1 3 ? 0.664 24.755 12.452 1.00 2.18 ? 3 ASN A O 1
ATOM 15 C CB . ASN A 1 3 ? 2.476 24.373 15.080 1.00 1.83 ? 3 ASN A CB 1
ATOM 16 C CG . ASN A 1 3 ? 3.085 24.989 16.330 1.00 2.00 ? 3 ASN A CG 1
ATOM 17 O OD1 . ASN A 1 3 ? 4.269 24.769 16.627 1.00 9.96 ? 3 ASN A OD1 1
ATOM 18 N ND2 . ASN A 1 3 ? 2.316 25.785 17.055 1.00 5.13 ? 3 ASN A ND2 1
ATOM 19 N N . GLN A 1 4 ? 2.678 24.238 11.700 1.00 4.45 ? 4 GLN A N 1
ATOM 20 C CA . GLN A 1 4 ? 2.184 23.550 10.509 1.00 3.39 ? 4 GLN A CA 1
ATOM 21 C C . GLN A 1 4 ? 2.899 22.223 10.328 1.00 2.04 ? 4 GLN A C 1
ATOM 22 O O . GLN A 1 4 ? 4.140 22.071 10.430 1.00 0.12 ? 4 GLN A O 1
ATOM 23 C CB . GLN A 1 4 ? 2.369 24.421 9.272 1.00 6.63 ? 4 GLN A CB 1
ATOM 24 C CG . GLN A 1 4 ? 1.691 23.888 8.022 1.00 1.39 ? 4 GLN A CG 1
ATOM 25 C CD . GLN A 1 4 ? 1.991 24.745 6.803 1.00 4.34 ? 4 GLN A CD 1
ATOM 26 O OE1 . GLN A 1 4 ? 3.183 24.831 6.461 1.00 3.23 ? 4 GLN A OE1 1
ATOM 27 N NE2 . GLN A 1 4 ? 1.043 25.357 6.123 1.00 0.45 ? 4 GLN A NE2 1
ATOM 28 N N . ASN A 1 5 ? 2.112 21.173 10.084 1.00 0.09 ? 5 ASN A N 1
ATOM 29 C CA . ASN A 1 5 ? 2.651 19.846 9.815 1.00 2.42 ? 5 ASN A CA 1
ATOM 30 C C . ASN A 1 5 ? 2.254 19.479 8.384 1.00 0.08 ? 5 ASN A C 1
ATOM 31 O O . ASN A 1 5 ? 1.039 19.403 8.168 1.00 2.03 ? 5 ASN A O 1
ATOM 32 C CB . ASN A 1 5 ? 2.134 18.813 10.809 1.00 3.76 ? 5 ASN A CB 1
ATOM 33 C CG . ASN A 1 5 ? 2.548 18.996 12.249 1.00 3.78 ? 5 ASN A CG 1
ATOM 34 O OD1 . ASN A 1 5 ? 3.731 18.787 12.574 1.00 6.41 ? 5 ASN A OD1 1
ATOM 35 N ND2 . ASN A 1 5 ? 1.663 19.359 13.159 1.00 6.64 ? 5 ASN A ND2 1
ATOM 36 N N . ASN A 1 6 ? 3.197 19.266 7.485 1.00 5.08 ? 6 ASN A N 1
ATOM 37 C CA . ASN A 1 6 ? 2.922 18.857 6.113 1.00 0.40 ? 6 ASN A CA 1
ATOM 38 C C . ASN A 1 6 ? 3.395 17.427 5.919 1.00 0.08 ? 6 ASN A C 1
ATOM 39 O O . ASN A 1 6 ? 4.578 17.213 5.622 1.00 0.08 ? 6 ASN A O 1
ATOM 40 C CB . ASN A 1 6 ? 3.595 19.774 5.086 1.00 0.71 ? 6 ASN A CB 1
ATOM 41 C CG . ASN A 1 6 ? 3.264 21.223 5.407 1.00 1.54 ? 6 ASN A CG 1
ATOM 42 O OD1 . ASN A 1 6 ? 4.162 22.031 5.685 1.00 0.08 ? 6 ASN A OD1 1
ATOM 43 N ND2 . ASN A 1 6 ? 1.990 21.560 5.360 1.00 6.19 ? 6 ASN A ND2 1
ATOM 44 N N . PHE A 1 7 ? 2.564 16.413 6.100 1.00 0.08 ? 7 PHE A N 1
ATOM 45 C CA . PHE A 1 7 ? 2.941 15.023 5.907 1.00 0.08 ? 7 PHE A CA 1
ATOM 46 C C . PHE A 1 7 ? 3.109 14.697 4.440 1.00 0.79 ? 7 PHE A C 1
ATOM 47 O O . PHE A 1 7 ? 3.786 13.632 4.230 1.00 5.35 ? 7 PHE A O 1
ATOM 48 C CB . PHE A 1 7 ? 1.846 14.141 6.527 1.00 0.08 ? 7 PHE A CB 1
ATOM 49 C CG . PHE A 1 7 ? 1.860 14.227 8.026 1.00 0.90 ? 7 PHE A CG 1
ATOM 50 C CD1 . PHE A 1 7 ? 2.665 13.471 8.827 1.00 0.08 ? 7 PHE A CD1 1
ATOM 51 C CD2 . PHE A 1 7 ? 1.035 15.165 8.667 1.00 1.31 ? 7 PHE A CD2 1
ATOM 52 C CE1 . PHE A 1 7 ? 2.732 13.481 10.201 1.00 0.08 ? 7 PHE A CE1 1
ATOM 53 C CE2 . PHE A 1 7 ? 1.073 15.196 10.044 1.00 0.08 ? 7 PHE A CE2 1
ATOM 54 C CZ . PHE A 1 7 ? 1.913 14.429 10.837 1.00 4.13 ? 7 PHE A CZ 1
ATOM 55 O OXT . PHE A 1 7 ? 2.697 15.269 3.478 1.00 3.61 ? 7 PHE A OXT 1
HETATM 56 ZN ZN . ZN B 2 . ? 2.274 28.998 19.674 1.00 3.34 ? 101 ZN A ZN 1
HETATM 57 C C . ACT C 3 . ? -0.344 27.222 20.022 1.00 9.18 ? 102 ACT A C 1
HETATM 58 O O . ACT C 3 . ? 0.367 28.256 19.789 1.00 0.08 ? 102 ACT A O 1
HETATM 59 O OXT . ACT C 3 . ? -1.608 27.244 19.853 1.00 4.95 ? 102 ACT A OXT 1
HETATM 60 C CH3 . ACT C 3 . ? 0.296 25.894 20.494 1.00 4.49 ? 102 ACT A CH3 1
HETATM 61 O O . HOH D 4 . ? 5.941 17.825 3.335 1.00 6.22 ? 201 HOH A O 1
#