data_1B2J

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1B2J
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1B2J
_pdbx_vrpt_summary.PDB_deposition_date         1998-11-27
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2023-08-09
_pdbx_vrpt_summary.report_creation_date        2023-08-02:12:37
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,mogul,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      "PROTEIN (RUBREDOXIN)"  
2  non-polymer  "FE (III) ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.6  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      
#
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   94.09  141614     ?     ?  
2  2  1   91.68    3665  1.60  1.60  
3  1  2  100.00  138981     ?     ?  
4  2  2  100.00    3564  1.60  1.60  
5  1  3   29.53  138945     ?     ?  
6  2  3    9.09    3563  1.60  1.60  
#
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   29.53  
4  6  3  A  1  1  A    9.09  
#
_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      1.33
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.81
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   434
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  590
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       4.17
_pdbx_vrpt_summary_geometry.clashscore                     1.25
_pdbx_vrpt_summary_geometry.num_H_reduce                   376
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 434
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.81
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                590
_pdbx_vrpt_summary_geometry.angles_RMSZ                    1.33
#
_pdbx_vrpt_summary_diffraction.exp_method           x-ray
_pdbx_vrpt_summary_diffraction.ordinal              1
_pdbx_vrpt_summary_diffraction.PDB_resolution_high  1.60
_pdbx_vrpt_summary_diffraction.PDB_resolution_low   30.00
_pdbx_vrpt_summary_diffraction.PDB_R                0.18
_pdbx_vrpt_summary_diffraction.PDB_Rfree            0.23
#
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
_pdbx_vrpt_model_instance.count_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.count_plane_outliers
 1  1  1  A   1  MET  A   1  .  ?        ?     ?     ?  
 2  1  1  A   2  LYS  A   2  .  ?        ?     ?     ?  
 3  1  1  A   3  LYS  A   3  .  ?        ?     ?     ?  
 4  1  1  A   4  TYR  A   4  .  ?        ?     1     ?  
 5  1  1  A   5  THR  A   5  .  ?        ?     ?     ?  
 6  1  1  A   6  CYS  A   6  .  ?        ?     ?     ?  
 7  1  1  A   7  THR  A   7  .  ?        ?     ?     ?  
 8  1  1  A   8  VAL  A   8  .  ?        ?     ?     ?  
 9  1  1  A   9  CYS  A   9  .  ?        ?     ?     1  
10  1  1  A  10  GLY  A  10  .  ?        ?     ?     ?  
11  1  1  A  11  TYR  A  11  .  ?        ?     ?     ?  
12  1  1  A  12  ILE  A  12  .  ?        ?     ?     ?  
13  1  1  A  13  TYR  A  13  .  ?        ?     ?     ?  
14  1  1  A  14  ASN  A  14  .  ?        ?     ?     ?  
15  1  1  A  15  PRO  A  15  .  ?        ?     ?     ?  
16  1  1  A  16  GLU  A  16  .  ?        ?     ?     ?  
17  1  1  A  17  ASP  A  17  .  ?        ?     ?     ?  
18  1  1  A  18  GLY  A  18  .  ?        ?     ?     ?  
19  1  1  A  19  ASP  A  19  .  ?        1     ?     ?  
20  1  1  A  20  PRO  A  20  .  ?        ?     ?     ?  
21  1  1  A  21  ASP  A  21  .  ?        ?     ?     ?  
22  1  1  A  22  ASN  A  22  .  ?        ?     ?     ?  
23  1  1  A  23  GLY  A  23  .  ?        ?     ?     ?  
24  1  1  A  24  VAL  A  24  .  ?        ?     ?     ?  
25  1  1  A  25  ASN  A  25  .  ?        ?     ?     ?  
26  1  1  A  26  PRO  A  26  .  ?        ?     ?     ?  
27  1  1  A  27  GLY  A  27  .  ?        ?     ?     ?  
28  1  1  A  28  THR  A  28  .  ?        ?     ?     ?  
29  1  1  A  29  ASP  A  29  .  ?        ?     ?     ?  
30  1  1  A  30  PHE  A  30  .  ?        ?     ?     ?  
31  1  1  A  31  LYS  A  31  .  ?        ?     ?     ?  
32  1  1  A  32  ASP  A  32  .  ?        ?     ?     ?  
33  1  1  A  33  ILE  A  33  .  ?        ?     ?     ?  
34  1  1  A  34  PRO  A  34  .  ?        ?     ?     ?  
35  1  1  A  35  ASP  A  35  .  ?        1     ?     ?  
36  1  1  A  36  ASP  A  36  .  ?        2     ?     ?  
37  1  1  A  37  TRP  A  37  .  ?        ?     ?     ?  
38  1  1  A  38  VAL  A  38  .  ?        ?     ?     ?  
39  1  1  A  39  CYS  A  39  .  ?        ?     ?     ?  
40  1  1  A  40  PRO  A  40  .  ?        ?     ?     ?  
41  1  1  A  41  LEU  A  41  .  ?        ?     ?     ?  
42  1  1  A  42  CYS  A  42  .  ?        ?     ?     ?  
43  1  1  A  43  ALA  A  43  .  ?        ?     ?     ?  
44  1  1  A  44  VAL  A  44  .  ?        ?     ?     ?  
45  1  1  A  45  GLY  A  45  .  ?        ?     ?     ?  
46  1  1  A  46  LYS  A  46  .  ?        ?     ?     ?  
47  1  1  A  47  ASP  A  47  .  ?        ?     ?     ?  
48  1  1  A  48  GLN  A  48  .  ?        ?     ?     ?  
49  1  1  A  49  PHE  A  49  .  ?        ?     ?     ?  
50  1  1  A  50  GLU  A  50  .  ?        ?     ?     ?  
51  1  1  A  51  GLU  A  51  .  ?        ?     1     ?  
52  1  1  A  52  VAL  A  52  .  ?        ?     ?     ?  
53  1  1  A  53  GLU  A  53  .  ?        ?     ?     ?  
54  1  1  A  54  GLU  A  54  .  ?        ?     ?     ?  
55  1  2  B   .  FE   A  55  .  ?        ?     ?     ?  
56  1  3  C   .  HOH  A  56  .  ?        ?     ?     ?  
57  1  3  C   .  HOH  A  57  .  ?        ?     ?     ?  
58  1  3  C   .  HOH  A  58  .  ?        ?     ?     ?  
59  1  3  C   .  HOH  A  59  .  ?        ?     ?     ?  
60  1  3  C   .  HOH  A  60  .  ?        ?     ?     ?  
61  1  3  C   .  HOH  A  61  .  ?        ?     ?     ?  
62  1  3  C   .  HOH  A  62  .  ?        ?     ?     ?  
63  1  3  C   .  HOH  A  63  .  ?        ?     ?     ?  
64  1  3  C   .  HOH  A  64  .  ?        ?     ?     ?  
65  1  3  C   .  HOH  A  65  .  ?        ?     ?     ?  
66  1  3  C   .  HOH  A  66  .  ?        ?     ?     ?  
67  1  3  C   .  HOH  A  67  .  ?        ?     ?     ?  
68  1  3  C   .  HOH  A  68  .  ?        ?     ?     ?  
69  1  3  C   .  HOH  A  69  .  ?        ?     ?     ?  
70  1  3  C   .  HOH  A  70  .  ?        ?     ?     ?  
71  1  3  C   .  HOH  A  71  .  ?        ?     ?     ?  
72  1  3  C   .  HOH  A  72  .  ?        ?     ?     ?  
73  1  3  C   .  HOH  A  73  .  ?        ?     ?     ?  
74  1  3  C   .  HOH  A  74  .  ?        ?     ?     ?  
75  1  3  C   .  HOH  A  75  .  ?        ?     ?     ?  
76  1  3  C   .  HOH  A  76  .  ?        ?     ?     ?  
77  1  3  C   .  HOH  A  77  .  ?        ?     ?     ?  
78  1  3  C   .  HOH  A  78  .  ?        ?     ?     ?  
79  1  3  C   .  HOH  A  79  .  ?        ?     ?     ?  
80  1  3  C   .  HOH  A  80  .  ?        ?     ?     ?  
81  1  3  C   .  HOH  A  81  .  ?        ?     ?     ?  
82  1  3  C   .  HOH  A  82  .  ?        ?     ?     ?  
83  1  3  C   .  HOH  A  83  .  ?        ?     ?     ?  
84  1  3  C   .  HOH  A  84  .  ?        ?     ?     ?  
85  1  3  C   .  HOH  A  85  .  ?        ?     ?     ?  
86  1  3  C   .  HOH  A  86  .  ?        ?     ?     ?  
87  1  3  C   .  HOH  A  87  .  ?        ?     ?     ?  
88  1  3  C   .  HOH  A  88  .  ?        ?     ?     ?  
89  1  3  C   .  HOH  A  89  .  ?        ?     ?     ?  
90  1  3  C   .  HOH  A  90  .  ?        ?     ?     ?  
91  1  3  C   .  HOH  A  91  .  ?        ?     ?     ?  
92  1  3  C   .  HOH  A  92  .  ?        ?     ?     ?  
#
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.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
 1   1  mtm           ?       ?  ?        11   8  0.67  10  0.76  molprobity  
 2   2  mttm      -93.3   152.7  Favored  13   9  0.40  11  0.74  molprobity  
 3   3  mttt      -83.5   143.2  Favored  13   9  0.64  11  0.84  molprobity  
 4   4  m-85     -117.8   148.1  Favored   9  13  1.14  18  1.36  molprobity  
 5   5  t        -120.8   136.2  Favored   7   7  1.32  10  0.82  molprobity  
 6   6  t         -66.9   114.5  Favored   4   6  1.12   8  1.34  molprobity  
 7   7  p         -76.0    -9.4  Favored   7   7  1.38  10  1.63  molprobity  
 8   8  t         -83.3   -41.6  Favored   9   7  0.85  10  1.01  molprobity  
 9   9  p        -130.6    -4.1  Favored   4   6  0.74   8  1.86  molprobity  
10  10  ?          89.1    -3.0  Favored   3   4  0.93   5  1.20  molprobity  
11  11  t80       -52.1   142.7  Favored   9  13  0.64  18  0.78  molprobity  
12  12  mp       -113.1   121.7  Favored  11   8  0.71  11  1.16  molprobity  
13  13  t80       -85.4   118.8  Favored   9  13  0.85  18  1.76  molprobity  
14  14  t-20     -107.7   116.0  Favored   6   8  0.93  12  1.09  molprobity  
15  15  Cg_endo   -60.1   -26.9  Favored   7   8  0.46  11  0.68  molprobity  
16  16  mt-10     -65.6   -32.1  Favored   6   9  0.49  12  1.00  molprobity  
17  17  m-20      -91.8   -35.0  Favored   4   8  0.85  11  0.99  molprobity  
18  18  ?          66.8  -154.3  Favored   3   4  0.90   5  1.93  molprobity  
19  19  t0       -145.1    64.9  Favored   4   8  0.81  12  2.66  molprobity  
20  20  Cg_endo   -58.6   -31.9  Favored   7   8  1.09  11  1.42  molprobity  
21  21  m-20      -62.0   -26.6  Favored   4   8  0.25  11  1.04  molprobity  
22  22  m-80     -108.1    24.6  Favored   6   8  0.75  11  1.19  molprobity  
23  23  ?          85.4     7.7  Favored   3   4  0.89   5  1.24  molprobity  
24  24  t        -103.8   104.4  Favored   9   7  0.42  10  1.10  molprobity  
25  25  m-20      -74.3   156.5  Favored   6   8  0.93  12  1.04  molprobity  
26  26  Cg_exo    -50.0   140.6  Favored   7   8  1.06  11  1.11  molprobity  
27  27  ?          90.2     6.0  Favored   3   4  0.61   5  0.65  molprobity  
28  28  m         -88.4   121.1  Favored   7   7  0.72  10  1.17  molprobity  
29  29  t0        -66.0   145.0  Favored   4   8  0.78  11  1.72  molprobity  
30  30  t80       -55.5   -35.7  Favored   9  12  1.14  16  1.63  molprobity  
31  31  pttp      -64.5   -27.0  Favored  13   9  0.67  11  0.81  molprobity  
32  32  m-20      -87.7    -8.6  Favored   4   8  0.78  11  1.70  molprobity  
33  33  mt        -63.7   131.5  Favored  11   8  0.86  12  1.09  molprobity  
34  34  Cg_exo    -48.4   138.8  Favored   7   8  0.57  11  0.84  molprobity  
35  35  m-20      -73.0     0.2  Favored   4   8  1.24  11  2.43  molprobity  
36  36  p-10      -99.0     7.7  Favored   4   8  1.16  11  2.40  molprobity  
37  37  t90       -74.5   143.8  Favored  10  16  0.63  23  0.81  molprobity  
38  38  m        -126.8   154.8  Favored   9   7  0.67  10  1.35  molprobity  
39  39  t         -52.2   131.0  Favored   4   6  0.66   9  1.52  molprobity  
40  40  Cg_endo   -64.1   -25.9  Favored   7   8  0.84  11  1.09  molprobity  
41  41  mt        -93.4   -41.0  Favored  11   8  0.64  11  1.37  molprobity  
42  42  p        -118.3    -4.3  Favored   4   6  0.14   8  0.34  molprobity  
43  43  ?          67.8    22.8  Favored   5   5  0.79   7  1.49  molprobity  
44  44  m         -88.1   158.9  Favored   9   7  0.60  10  1.31  molprobity  
45  45  ?         -76.7   174.7  Favored   3   4  1.38   5  2.66  molprobity  
46  46  mtpt      -56.7   -26.4  Favored  13   9  0.84  11  0.91  molprobity  
47  47  p-10      -69.7    -8.3  Favored   4   8  0.58  11  1.75  molprobity  
48  48  mm-40    -101.2    11.5  Favored   8   9  0.42  12  0.52  molprobity  
49  49  m-85      -99.3   152.3  Favored   9  12  0.84  16  1.59  molprobity  
50  50  mt-10    -137.7   149.0  Favored   6   9  0.64  12  0.85  molprobity  
51  51  mt-10     -59.2   138.5  Favored   6   9  0.59  12  1.12  molprobity  
52  52  t         -90.0    96.8  Favored   9   7  0.44  10  1.00  molprobity  
53  53  OUTLIER   -95.9   153.4  Favored   6   9  0.44  12  0.82  molprobity  
54  54  OUTLIER       ?       ?  ?         6   9  0.59   9  0.67  molprobity  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
1   4  CZ   1  0.53  2.44  
2  51  HG3  1  0.53  2.44  
#
_pdbx_vrpt_instance_intra_plane_outliers.ordinal      1
_pdbx_vrpt_instance_intra_plane_outliers.instance_id  9
_pdbx_vrpt_instance_intra_plane_outliers.type         mainchain
_pdbx_vrpt_instance_intra_plane_outliers.improper     -12.14
#
loop_
_pdbx_vrpt_instance_intra_angle_outliers.ordinal
_pdbx_vrpt_instance_intra_angle_outliers.instance_id
_pdbx_vrpt_instance_intra_angle_outliers.atom_1
_pdbx_vrpt_instance_intra_angle_outliers.atom_2
_pdbx_vrpt_instance_intra_angle_outliers.atom_3
_pdbx_vrpt_instance_intra_angle_outliers.obs
_pdbx_vrpt_instance_intra_angle_outliers.mean
_pdbx_vrpt_instance_intra_angle_outliers.stdev
_pdbx_vrpt_instance_intra_angle_outliers.Z
1  19  CB  CG  OD2  125.099  118.300  0.900   7.55  
2  35  CB  CG  OD1  123.421  118.300  0.900   5.69  
3  36  CB  CG  OD1  123.254  118.300  0.900   5.50  
4  36  CB  CG  OD2  113.187  118.300  0.900  -5.68  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  mogul        unknown                                                               Y  
3  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
