data_9EG5

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.069
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_entry.id  9EG5
#
loop_
_entity.id
1  
2  
3  
4  
5  
#
loop_
_struct_asym.id
_struct_asym.entity_id
A  1  
B  2  
C  3  
D  4  
E  5  
#
_pdbx_vrpt_database.id             PDB
_pdbx_vrpt_database.code           9EG5
_pdbx_vrpt_database.extended_code  pdb_00009eg5
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    9EG5
_pdbx_vrpt_summary.extended_entry_id           pdb_00009eg5
_pdbx_vrpt_summary.PDB_deposition_date         2024-11-20
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2025-05-21
_pdbx_vrpt_summary.report_creation_date        2025-05-12:16:58
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,validation_schema,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "Co-MAHF-9 A8S"  
2  non-polymer  "COBALT (II) ION"  
3  non-polymer  METHANOL  
4  non-polymer  ACETONITRILE  
5  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
E  5  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  0.98  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
4  RSRZ_outliers_percent         
5  R_value_R_free                
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
 1  1  1   99.96  180529     ?     ?  
 2  2  1  100.00    1154  0.94  1.02  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1094  0.94  1.02  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1095  0.94  1.02  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1025  0.94  1.02  
 9  1  5   99.37  164625     ?     ?  
10  2  5   78.37    1026  0.94  1.02  
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
1  3  2  A  1  1  A  100.00  
2  4  2  A  1  1  A  100.00  
3  5  3  A  1  1  A  100.00  
4  6  3  A  1  1  A  100.00  
5  7  4  A  1  1  A  100.00  
6  8  4  A  1  1  A  100.00  
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     A
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      0.74
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.75
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   50
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  67
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       0.00
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   78
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 50
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.75
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                67
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.74
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            44.309
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         7.680
_pdbx_vrpt_summary_diffraction.I_over_sigma              3.75(0.98A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3615
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.431
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.470
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.307
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.977
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1146
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1389
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1250
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.98
_pdbx_vrpt_summary_diffraction.EDS_res_low               20.48
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[7.039,8.693,7.755,0.000,-1.860,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.211
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 32.29 % of the origin peak, indicating pseudo-translational symmetry.  The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 9.6223e-04."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         1
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         88.83
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      3281
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.06
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       0.98
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        20.48
_pdbx_vrpt_summary_diffraction.PDB_R                     0.1163
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.1378
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.12
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.006 (Gargrove)"
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
 1  1  1  A   1  ACE  A    1  .  ?     
 2  1  1  A   2  LEU  A    2  .  ?     
 3  1  1  A   3  AIB  A    3  .  ?     
 4  1  1  A   4  GLU  A    4  .  ?     
 5  1  1  A   5  AIB  A    5  .  ?     
 6  1  1  A   6  LEU  A    6  .  ?     
 7  1  1  A   7  HIS  A    7  .  ?     
 8  1  1  A   8  SER  A    8  .  ?     
 9  1  1  A   9  AIB  A    9  .  ?     
10  1  1  A  10  LEU  A   10  .  ?     
11  1  1  A  11  NH2  A   11  .  ?     
12  1  2  B   .  CO   A  101  .  ?     
13  1  3  C   .  MOH  A  102  .  ?     
14  1  4  D   .  CCN  A  103  .  ?     
15  1  5  E   .  HOH  A  201  .  ?     
16  1  5  E   .  HOH  A  202  .  ?     
17  1  5  E   .  HOH  A  203  .  ?     
18  1  5  E   .  HOH  A  204  .  ?     
19  1  5  E   .  HOH  A  205  .  ?     
20  1  5  E   .  HOH  A  206  .  ?     
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.OWAB
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
_pdbx_vrpt_model_instance_geometry.average_occupancy
 1   1  ?          ?      ?  ?           3   7.820     1  4.33     2  0.38  molprobity  1.000  
 2   2  tp     -56.8  -48.9  Favored    11   8.350     7  0.53     8  0.67  molprobity  1.000  
 3   3  ?          ?      ?  ?           7   7.520     1  1.08     0     ?  mogul       1.000  
 4   4  mm-30  -80.4  -28.1  Favored     6   9.890     8  0.32     9  0.66  molprobity  1.000  
 5   5  ?          ?      ?  ?           7   8.020     1  1.09     0     ?  mogul       1.000  
 6   6  mt     -70.8  -45.1  Favored    11   9.560     8  0.34    11  1.21  molprobity  1.000  
 7   7  m170   -65.0  -32.4  Favored     7   8.600    11  0.64    15  0.56  molprobity  1.000  
 8   8  m      -65.9  -45.7  Favored     5   7.820     5  0.25     5  0.25  molprobity  1.000  
 9   9  ?          ?      ?  ?           7  10.630     1  0.94     0     ?  mogul       1.000  
10  10  mt     -81.8  -19.7  Favored    11  11.710     7  0.24     8  0.61  molprobity  1.000  
11  11  ?          ?      ?  ?           ?  12.030     ?     ?     ?     ?  ?           1.000  
12  12  ?          ?      ?  ?           ?   4.610     ?     ?     ?     ?  ?           0.500  
13  13  ?          ?      ?  ?           ?  26.630     1  0.07     ?     ?  mogul       1.000  
14  14  ?          ?      ?  ?           3  21.020     2  0.12     1  0.62  mogul       1.000  
15  15  ?          ?      ?  ?           ?  30.000     ?     ?     ?     ?  ?           1.000  
16  16  ?          ?      ?  ?           ?  33.850     ?     ?     ?     ?  ?           1.000  
17  17  ?          ?      ?  ?           ?  25.570     ?     ?     ?     ?  ?           1.000  
18  18  ?          ?      ?  ?           ?  34.820     ?     ?     ?     ?  ?           1.000  
19  19  ?          ?      ?  ?           ?  15.130     ?     ?     ?     ?  ?           1.000  
20  20  ?          ?      ?  ?           ?  35.880     ?     ?     ?     ?  ?           1.000  
#
loop_
_pdbx_vrpt_model_instance_density.ordinal
_pdbx_vrpt_model_instance_density.instance_id
_pdbx_vrpt_model_instance_density.natoms_eds
_pdbx_vrpt_model_instance_density.RSRCC
_pdbx_vrpt_model_instance_density.RSR
_pdbx_vrpt_model_instance_density.RSRZ
_pdbx_vrpt_model_instance_density.EDIAm
_pdbx_vrpt_model_instance_density.OPIA
 1   1   6  0.970  0.053       ?  0.823   66.670  
 2   2  19  0.988  0.051  -0.068  0.867   62.500  
 3   3  13  0.989  0.032       ?  0.824   66.670  
 4   4  15  0.979  0.057  -0.456  0.813   66.670  
 5   5  13  0.992  0.030       ?  0.792   50.000  
 6   6  19  0.973  0.059   0.272  0.841   62.500  
 7   7  17  0.959  0.067   0.404  0.792   50.000  
 8   8  11  0.992  0.026  -0.890  0.885  100.000  
 9   9  13  0.987  0.041       ?  0.870   83.330  
10  10  19  0.980  0.060   0.315  0.731   25.000  
11  11   3  0.957  0.071       ?  0.872  100.000  
12  12   1  0.997  0.015       ?  0.970  100.000  
13  13   6  0.885  0.118       ?  0.625    0.000  
14  14   6  0.840  0.137       ?  0.692   33.330  
15  15   1  0.943  0.084       ?  0.622    0.000  
16  16   1  0.904  0.112       ?  0.412    0.000  
17  17   1  0.979  0.092       ?  0.891  100.000  
18  18   1  0.896  0.099       ?  0.288    0.000  
19  19   1  0.991  0.035       ?  0.837  100.000  
20  20   1  0.903  0.102       ?  0.377    0.000  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   "4-5-2 with Phenix2.0rc1"                                             Y  
2  mogul        "2022.3.0, CSD as543be (2022)"                                        Y  
3  eds          3.0                                                                   Y  
4  dcc          '"2.31  (2025-03-10))"'                                               Y  
5  xtriage      2.0rc1                                                                Y  
6  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
