data_9MDG

_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  9MDG
#
loop_
_entity.id
1  
2  
3  
4  
#
loop_
_struct_asym.id
_struct_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  3  
F  4  
G  4  
#
_pdbx_vrpt_database.id             PDB
_pdbx_vrpt_database.code           9MDG
_pdbx_vrpt_database.extended_code  pdb_00009mdg
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    9MDG
_pdbx_vrpt_summary.extended_entry_id           pdb_00009mdg
_pdbx_vrpt_summary.PDB_deposition_date         2024-12-05
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2025-05-21
_pdbx_vrpt_summary.report_creation_date        2025-05-12:16:31
_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 A8L"  
2  non-polymer  "COBALT (II) ION"  
3  non-polymer  METHANOL  
4  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  3  
F  4  
G  4  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  1.41  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   99.97    3801  1.40  1.44  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    3734  1.40  1.44  
 5  1  3    1.52  177891     ?     ?  
 6  2  3    0.03    3733  1.40  1.44  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    3499  1.40  1.44  
 9  1  5   84.05  164625     ?     ?  
10  2  5   45.06    3500  1.40  1.44  
#
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    2.42  
 4  6  3  A  1  1  A    0.03  
 5  7  4  A  1  1  A  100.00  
 6  8  4  A  1  1  A  100.00  
 7  3  2  B  1  1  B  100.00  
 8  4  2  B  1  1  B  100.00  
 9  5  3  B  1  1  B    1.52  
10  6  3  B  1  1  B    0.03  
11  7  4  B  1  1  B  100.00  
12  8  4  B  1  1  B  100.00  
#
loop_
_pdbx_vrpt_summary_entity_geometry.ordinal
_pdbx_vrpt_summary_entity_geometry.PDB_model_num
_pdbx_vrpt_summary_entity_geometry.entity_id
_pdbx_vrpt_summary_entity_geometry.label_asym_id
_pdbx_vrpt_summary_entity_geometry.auth_asym_id
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ
1  1  1  A  A  0.60  0.72  60  81  
2  1  1  B  B  0.70  0.82  52  70  
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       16.67
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   172
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 112
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.77
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                151
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.65
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            49.747
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         12.141
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.89(1.41A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2621
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.379
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.544
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.392
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.976
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1446
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1972
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1621
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.41
_pdbx_vrpt_summary_diffraction.EDS_res_low               17.26
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[14.961,11.206,11.313,0.000,2.052,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.301
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 52.42 % 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 4.8776e-05. The detected translational NCS is most likely also responsible for the elevated intensity ratio.  See the relevant section of the logfile for more details."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         5
_pdbx_vrpt_summary_diffraction.centric_outliers          1
_pdbx_vrpt_summary_diffraction.data_completeness         90.02
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      2386
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.11
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.41
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        17.26
_pdbx_vrpt_summary_diffraction.PDB_R                     0.1501
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.1971
_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  A  ?     
 7  1  1  A   6  LEU  A    6  B  ?     
 8  1  1  A   7  HIS  A    7  .  ?     
 9  1  1  A   8  LEU  A    8  .  ?     
10  1  1  A   9  AIB  A    9  .  ?     
11  1  1  A  10  LEU  A   10  .  ?     
12  1  1  A  11  NH2  A   11  .  ?     
13  1  1  B   1  ACE  B    1  .  ?     
14  1  1  B   2  LEU  B    2  .  ?     
15  1  1  B   3  AIB  B    3  .  ?     
16  1  1  B   4  GLU  B    4  .  ?     
17  1  1  B   5  AIB  B    5  .  ?     
18  1  1  B   6  LEU  B    6  .  ?     
19  1  1  B   7  HIS  B    7  .  ?     
20  1  1  B   8  LEU  B    8  .  ?     
21  1  1  B   9  AIB  B    9  .  ?     
22  1  1  B  10  LEU  B   10  .  ?     
23  1  1  B  11  NH2  B   11  .  ?     
24  1  2  C   .  CO   A  101  .  ?     
25  1  2  D   .  CO   A  102  .  ?     
26  1  3  E   .  MOH  B  101  .  ?     
27  1  4  F   .  HOH  A  201  .  ?     
28  1  4  F   .  HOH  A  202  .  ?     
29  1  4  F   .  HOH  A  203  .  ?     
30  1  4  F   .  HOH  A  204  .  ?     
31  1  4  F   .  HOH  A  205  .  ?     
32  1  4  G   .  HOH  B  201  .  ?     
33  1  4  G   .  HOH  B  202  .  ?     
34  1  4  G   .  HOH  B  203  .  ?     
35  1  4  G   .  HOH  B  204  .  ?     
36  1  4  G   .  HOH  B  205  .  ?     
37  1  4  G   .  HOH  B  206  .  ?     
38  1  4  G   .  HOH  B  207  .  ?     
39  1  4  G   .  HOH  B  208  .  ?     
40  1  4  G   .  HOH  B  209  .  ?     
#
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  12.650     1  4.65     2  0.49  molprobity  1.000  
 2   2  tp       -63.6  -51.3  Favored    11  19.390     7  0.46     8  0.56  molprobity  1.000  
 3   3  ?            ?      ?  ?           7  15.500     1  1.37     0     ?  mogul       1.000  
 4   4  mm-30    -61.7  -52.5  Favored     6  19.840     8  0.77     9  0.79  molprobity  1.000  
 5   5  ?            ?      ?  ?           7  20.030     1  1.50     0     ?  mogul       1.000  
 6   6  tp       -78.4  -23.2  Favored    11  23.560     8  0.24    11  0.27  molprobity  0.500  
 7   7  tp       -78.4  -23.2  Favored    11  23.560     8  0.24    11  0.27  molprobity  0.500  
 8   8  OUTLIER  -73.4  -30.3  Favored     6  15.700    11  0.27    15  0.88  molprobity  1.000  
 9   9  mt       -69.6  -46.9  Favored    11  22.050     7  0.21     8  0.54  molprobity  1.000  
10  10  ?            ?      ?  ?           7  14.930     1  1.49     0     ?  mogul       1.000  
11  11  mt       -85.3  -12.5  Favored    11  18.890     7  0.43     8  0.62  molprobity  1.000  
12  12  ?            ?      ?  ?           ?  20.400     ?     ?     ?     ?  ?           1.000  
13  13  ?            ?      ?  ?           3  15.360     1  4.84     2  0.28  molprobity  1.000  
14  14  tp       -50.8  -51.0  Favored    11  22.040     7  0.40     8  0.87  molprobity  1.000  
15  15  ?            ?      ?  ?           7  17.940     1  1.74     0     ?  mogul       1.000  
16  16  mm-30    -64.7  -51.4  Favored     6  20.930     8  0.71     9  0.60  molprobity  1.000  
17  17  ?            ?      ?  ?           7  21.560     1  0.85     0     ?  mogul       1.000  
18  18  mt       -70.8  -33.0  Favored    11  26.070     8  0.47    11  0.79  molprobity  1.000  
19  19  OUTLIER  -63.6  -30.2  Favored     7  14.650    11  0.25    15  0.80  molprobity  1.000  
20  20  mt       -70.6  -44.1  Favored    11  23.440     7  0.51     8  0.48  molprobity  1.000  
21  21  ?            ?      ?  ?           7  17.850     1  1.02     0     ?  mogul       1.000  
22  22  mt       -79.6  -16.4  Favored    11  20.270     7  0.49     8  0.51  molprobity  1.000  
23  23  ?            ?      ?  ?           ?  19.560     ?     ?     ?     ?  ?           1.000  
24  24  ?            ?      ?  ?           ?  10.390     ?     ?     ?     ?  ?           0.500  
25  25  ?            ?      ?  ?           ?   8.710     ?     ?     ?     ?  ?           0.500  
26  26  ?            ?      ?  ?           ?  67.470     1  0.06     ?     ?  mogul       1.000  
27  27  ?            ?      ?  ?           ?  25.450     ?     ?     ?     ?  ?           1.000  
28  28  ?            ?      ?  ?           ?  37.600     ?     ?     ?     ?  ?           1.000  
29  29  ?            ?      ?  ?           ?  16.180     ?     ?     ?     ?  ?           1.000  
30  30  ?            ?      ?  ?           ?  24.870     ?     ?     ?     ?  ?           1.000  
31  31  ?            ?      ?  ?           ?  46.050     ?     ?     ?     ?  ?           1.000  
32  32  ?            ?      ?  ?           ?  52.310     ?     ?     ?     ?  ?           1.000  
33  33  ?            ?      ?  ?           ?  23.360     ?     ?     ?     ?  ?           1.000  
34  34  ?            ?      ?  ?           ?  43.600     ?     ?     ?     ?  ?           1.000  
35  35  ?            ?      ?  ?           ?  18.200     ?     ?     ?     ?  ?           1.000  
36  36  ?            ?      ?  ?           ?  58.760     ?     ?     ?     ?  ?           1.000  
37  37  ?            ?      ?  ?           ?  33.610     ?     ?     ?     ?  ?           1.000  
38  38  ?            ?      ?  ?           ?  54.810     ?     ?     ?     ?  ?           1.000  
39  39  ?            ?      ?  ?           ?  35.060     ?     ?     ?     ?  ?           1.000  
40  40  ?            ?      ?  ?           ?  49.660     ?     ?     ?     ?  ?           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  0.940  0.063       ?  0.925   66.670  
 2   2  19  0.961  0.055  -0.406  0.932   87.500  
 3   3  13  0.962  0.057       ?  0.961  100.000  
 4   4  15  0.944  0.072  -0.480  0.894   77.780  
 5   5  13  0.966  0.076       ?  0.824   66.670  
 6   6  38  0.951  0.123   1.955  0.153   58.610  
 7   7  38  0.951  0.123   1.955  0.153   58.610  
 8   8  17  0.970  0.045  -0.636  1.001  100.000  
 9   9  19  0.974  0.053  -0.476  0.821   75.000  
10  10  13  0.963  0.055       ?  0.963  100.000  
11  11  19  0.959  0.061  -0.198  0.957  100.000  
12  12   3  0.975  0.045       ?  1.009  100.000  
13  13   6  0.971  0.044       ?  0.957  100.000  
14  14  19  0.954  0.056  -0.372  0.904   87.500  
15  15  13  0.970  0.050       ?  0.911   66.670  
16  16  15  0.945  0.070  -0.527  0.898   88.890  
17  17  13  0.946  0.065       ?  0.858   66.670  
18  18  19  0.951  0.064  -0.094  0.770   87.500  
19  19  17  0.964  0.048  -0.555  0.961  100.000  
20  20  19  0.958  0.072   0.184  0.774   62.500  
21  21  13  0.973  0.044       ?  0.978  100.000  
22  22  19  0.947  0.058  -0.302  0.978  100.000  
23  23   3  0.973  0.042       ?  0.955  100.000  
24  24   1  0.998  0.033       ?  0.693    0.000  
25  25   1  0.996  0.016       ?  0.716    0.000  
26  26   6  0.867  0.418       ?  0.014    0.000  
27  27   1  0.972  0.070       ?  0.835  100.000  
28  28   1  0.924  0.144       ?  0.662    0.000  
29  29   1  0.982  0.039       ?  0.979  100.000  
30  30   1  0.968  0.056       ?  0.899  100.000  
31  31   1  0.890  0.145       ?  0.232    0.000  
32  32   1  0.719  0.204       ?  0.452    0.000  
33  33   1  0.968  0.079       ?  0.975  100.000  
34  34   1  0.870  0.119       ?  0.399    0.000  
35  35   1  0.965  0.057       ?  0.867  100.000  
36  36   1  0.844  0.210       ?  0.103    0.000  
37  37   1  0.853  0.165       ?  0.618    0.000  
38  38   1  0.882  0.139       ?  0.071    0.000  
39  39   1  0.868  0.111       ?  0.436    0.000  
40  40   1  0.819  0.126       ?  0.000    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  
##
