data_3QII

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  3QII
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    3QII
_pdbx_vrpt_summary.PDB_deposition_date         2011-01-27
_pdbx_vrpt_summary.PDB_revision_number         6
_pdbx_vrpt_summary.PDB_revision_date           2023-09-13
_pdbx_vrpt_summary.report_creation_date        2023-09-02:16:58
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,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      "PHD finger protein 20"  
2  non-polymer  "UNKNOWN ATOM OR 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  2.3  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  141614     ?     ?  
 2  2  1  100.00    5643  2.30  2.30  
 3  1  2  100.00  138981     ?     ?  
 4  2  2  100.00    5575  2.30  2.30  
 5  1  3   51.52  138945     ?     ?  
 6  2  3   68.93    5575  2.30  2.30  
 7  1  4   66.49  127900     ?     ?  
 8  2  4   72.90    4938  2.30  2.30  
 9  1  5   19.18  130704     ?     ?  
10  2  5   24.70    5042  2.30  2.30  
#
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   51.52  
4  6  3  A  1  1  A   68.93  
5  7  4  A  1  1  A   66.49  
6  8  4  A  1  1  A   72.90  
#
_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      0.68
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.76
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   432
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  586
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       2.22
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   407
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 432
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.76
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                586
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.68
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 97.332
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            22.303
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         49.005
_pdbx_vrpt_summary_diffraction.I_over_sigma              4.88(2.31A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        5531
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.257
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.347
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.509
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.346
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.943
_pdbx_vrpt_summary_diffraction.DCC_R                     0.23
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.27
_pdbx_vrpt_summary_diffraction.EDS_R                     0.23
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.30
_pdbx_vrpt_summary_diffraction.EDS_res_low               28.00
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[54.334,54.334,41.331,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.260
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 13.10% of the height of the origin peak. No significant pseudotranslation is detected."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         0
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         99.46
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      266
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.81
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     1.92
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.30
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        30.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.24
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.27
#
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  21  GLU  A   86  .  ?     
 2  1  1  A  22  PHE  A   87  .  ?     
 3  1  1  A  23  GLN  A   88  .  ?     
 4  1  1  A  24  ILE  A   89  .  ?     
 5  1  1  A  25  ASN  A   90  .  ?     
 6  1  1  A  26  GLU  A   91  .  ?     
 7  1  1  A  27  GLN  A   92  .  ?     
 8  1  1  A  28  VAL  A   93  .  ?     
 9  1  1  A  29  LEU  A   94  .  ?     
10  1  1  A  30  ALA  A   95  .  ?     
11  1  1  A  31  CYS  A   96  .  ?     
12  1  1  A  32  TRP  A   97  .  ?     
13  1  1  A  33  SER  A   98  .  ?     
14  1  1  A  34  ASP  A   99  .  ?     
15  1  1  A  35  CYS  A  100  .  ?     
16  1  1  A  36  ARG  A  101  .  ?     
17  1  1  A  37  PHE  A  102  .  ?     
18  1  1  A  38  TYR  A  103  .  ?     
19  1  1  A  39  PRO  A  104  .  ?     
20  1  1  A  40  ALA  A  105  .  ?     
21  1  1  A  41  LYS  A  106  .  ?     
22  1  1  A  42  VAL  A  107  .  ?     
23  1  1  A  43  THR  A  108  .  ?     
24  1  1  A  44  ALA  A  109  .  ?     
25  1  1  A  45  VAL  A  110  .  ?     
26  1  1  A  46  ASN  A  111  .  ?     
27  1  1  A  47  LYS  A  112  .  ?     
28  1  1  A  48  ASP  A  113  .  ?     
29  1  1  A  49  GLY  A  114  .  ?     
30  1  1  A  50  THR  A  115  .  ?     
31  1  1  A  51  TYR  A  116  .  ?     
32  1  1  A  52  THR  A  117  .  ?     
33  1  1  A  53  VAL  A  118  .  ?     
34  1  1  A  54  LYS  A  119  .  ?     
35  1  1  A  55  PHE  A  120  .  ?     
36  1  1  A  56  TYR  A  121  .  ?     
37  1  1  A  57  ASP  A  122  .  ?     
38  1  1  A  58  GLY  A  123  .  ?     
39  1  1  A  59  VAL  A  124  .  ?     
40  1  1  A  60  VAL  A  125  .  ?     
41  1  1  A  61  GLN  A  126  .  ?     
42  1  1  A  62  THR  A  127  .  ?     
43  1  1  A  63  VAL  A  128  .  ?     
44  1  1  A  64  LYS  A  129  .  ?     
45  1  1  A  65  HIS  A  130  .  ?     
46  1  1  A  66  ILE  A  131  .  ?     
47  1  1  A  67  HIS  A  132  .  ?     
48  1  1  A  68  VAL  A  133  .  ?     
49  1  1  A  69  LYS  A  134  .  ?     
50  1  1  A  70  ALA  A  135  .  ?     
51  1  1  A  71  PHE  A  136  .  ?     
52  1  1  A  72  SER  A  137  .  ?     
53  1  2  B   .  UNX  A    1  .  ?     
54  1  3  C   .  HOH  A    2  .  ?     
55  1  3  C   .  HOH  A    3  .  ?     
56  1  3  C   .  HOH  A    4  .  ?     
57  1  3  C   .  HOH  A    5  .  ?     
58  1  3  C   .  HOH  A    6  .  ?     
59  1  3  C   .  HOH  A    7  .  ?     
60  1  3  C   .  HOH  A    8  .  ?     
61  1  3  C   .  HOH  A    9  .  ?     
62  1  3  C   .  HOH  A   10  .  ?     
63  1  3  C   .  HOH  A  151  .  ?     
#
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  mp0           ?      ?  ?           5  67.040     9  0.78    12  0.96  molprobity  1.000  
 2   2  m-85      -77.5  153.4  Favored     9  56.570    12  0.44    16  0.42  molprobity  1.000  
 3   3  mt-30    -115.4  166.8  Favored     8  69.160     9  0.65    12  0.32  molprobity  1.000  
 4   4  mt        -55.1  140.1  Favored    11  62.550     8  0.40    11  0.92  molprobity  1.000  
 5   5  m-20       74.3    5.2  Favored     6  63.960     8  0.35    11  0.58  molprobity  1.000  
 6   6  tt0       -88.7  147.5  Favored     6  64.160     9  1.24    12  0.84  molprobity  1.000  
 7   7  mt-30     -94.1  142.0  Favored     8  58.960     9  0.39    12  0.54  molprobity  1.000  
 8   8  m        -136.3  170.9  Favored     9  45.090     7  0.54    10  0.61  molprobity  1.000  
 9   9  mt        -96.1  125.4  Favored    11  41.320     8  0.49    11  0.73  molprobity  1.000  
10  10  ?        -121.6  146.8  Favored     5  35.210     5  0.47     7  0.52  molprobity  1.000  
11  11  t         -83.7  134.2  Favored     5  35.650     6  0.66     8  0.92  molprobity  1.000  
12  12  t90      -109.8  178.3  Favored    10  38.960    16  0.93    23  0.65  molprobity  1.000  
13  13  m         -61.9  -19.9  Favored     5  34.890     6  0.81     8  1.08  molprobity  1.000  
14  14  p-10      -87.9    4.2  Favored     4  36.310     8  0.52    11  0.70  molprobity  1.000  
15  15  OUTLIER    67.9   37.5  Favored     5  36.660     6  0.58     8  0.84  molprobity  1.000  
16  16  mtt85    -126.2  158.5  Favored    13  49.860    11  0.87    14  0.89  molprobity  1.000  
17  17  m-85      -97.1  141.6  Favored     9  36.800    12  0.60    16  0.42  molprobity  1.000  
18  18  m-85     -138.8  157.8  Favored     9  35.330    13  0.58    19  0.54  molprobity  1.000  
19  19  Cg_exo    -70.8  134.9  Favored     7  38.280     8  0.44    11  0.19  molprobity  1.000  
20  20  ?        -136.7  143.8  Favored     5  36.770     5  1.15     7  0.90  molprobity  1.000  
21  21  ttpt      -87.5  131.9  Favored    13  49.580     9  0.81    11  0.38  molprobity  1.000  
22  22  t         -70.5  118.4  Favored     9  43.030     7  0.81    10  0.68  molprobity  1.000  
23  23  p        -104.7  -18.0  Favored     7  43.660     7  0.62    10  0.60  molprobity  1.000  
24  24  ?        -155.7  140.9  Favored     5  42.530     5  0.83     7  0.85  molprobity  1.000  
25  25  t        -106.9  120.3  Favored     9  43.460     7  0.39    10  0.74  molprobity  1.000  
26  26  m-20     -103.4  146.4  Favored     6  40.960     8  0.55    11  0.59  molprobity  1.000  
27  27  mttp      -64.4  -22.5  Favored    13  41.880     9  0.89    11  0.64  molprobity  1.000  
28  28  p-10      -77.8    7.3  Favored     4  40.950     8  0.53    11  1.05  molprobity  1.000  
29  29  ?          85.7   14.7  Favored     3  41.280     4  0.49     5  0.82  molprobity  1.000  
30  30  p        -107.5  163.0  Favored     7  38.810     7  0.59    10  0.69  molprobity  1.000  
31  31  m-85     -121.9  146.9  Favored     9  42.430    13  0.88    18  0.81  molprobity  1.000  
32  32  m         -91.3  130.6  Favored     7  41.690     7  0.65    10  0.87  molprobity  1.000  
33  33  m        -130.9  156.2  Favored     9  36.400     7  0.93    10  0.65  molprobity  1.000  
34  34  ttpt     -130.6  121.8  Favored    13  46.620     9  0.84    11  0.57  molprobity  1.000  
35  35  m-85      -73.8  172.8  Favored     9  34.500    12  0.80    16  0.54  molprobity  1.000  
36  36  m-85      -60.6  -32.2  Favored     9  45.690    13  0.46    18  0.58  molprobity  1.000  
37  37  p-10      -80.2    1.6  Favored     4  43.730     8  0.37    11  0.63  molprobity  1.000  
38  38  ?          92.5   -0.0  Favored     3  46.270     4  0.48     5  0.18  molprobity  1.000  
39  39  t         -72.7  124.4  Favored     9  41.070     7  1.42    10  0.83  molprobity  1.000  
40  40  t        -103.2  144.8  Favored     9  43.460     7  0.61    10  0.76  molprobity  1.000  
41  41  tt0      -151.1  143.8  Favored     8  41.360     9  1.08    12  1.00  molprobity  1.000  
42  42  m        -102.5  133.2  Favored     7  39.930     7  0.60    10  0.77  molprobity  1.000  
43  43  m        -143.4  148.2  Favored     9  39.080     7  1.32    10  0.41  molprobity  1.000  
44  44  mttt      -72.6  146.6  Favored    13  48.500     9  1.25    11  0.60  molprobity  1.000  
45  45  t60       -52.9  -38.5  Favored     7  53.140    11  0.65    15  0.37  molprobity  1.000  
46  46  pt        -72.4  -10.3  Favored    11  45.960     8  0.94    11  0.62  molprobity  1.000  
47  47  m170     -106.7    7.9  Favored     7  38.050    11  0.37    15  0.34  molprobity  1.000  
48  48  m        -116.7  156.8  Favored     9  42.140     7  0.61    10  0.54  molprobity  1.000  
49  49  mtpt     -123.7  161.4  Favored    13  52.490     9  0.55    11  1.13  molprobity  1.000  
50  50  ?         -59.3  136.1  Favored     5  59.810     5  0.53     7  0.54  molprobity  1.000  
51  51  t80      -105.1  120.4  Favored     9  65.580    12  1.00    16  0.39  molprobity  1.000  
52  52  ?             ?      ?  ?           2  76.710     4  1.43     4  0.92  molprobity  1.000  
53  53  ?             ?      ?  ?           ?  30.000     ?     ?     ?     ?  ?           1.000  
54  54  ?             ?      ?  ?           ?  34.030     ?     ?     ?     ?  ?           1.000  
55  55  ?             ?      ?  ?           ?  35.060     ?     ?     ?     ?  ?           1.000  
56  56  ?             ?      ?  ?           ?  29.560     ?     ?     ?     ?  ?           1.000  
57  57  ?             ?      ?  ?           ?  48.700     ?     ?     ?     ?  ?           1.000  
58  58  ?             ?      ?  ?           ?  37.790     ?     ?     ?     ?  ?           1.000  
59  59  ?             ?      ?  ?           ?  50.910     ?     ?     ?     ?  ?           1.000  
60  60  ?             ?      ?  ?           ?  53.880     ?     ?     ?     ?  ?           1.000  
61  61  ?             ?      ?  ?           ?  39.240     ?     ?     ?     ?  ?           1.000  
62  62  ?             ?      ?  ?           ?  51.900     ?     ?     ?     ?  ?           1.000  
63  63  ?             ?      ?  ?           ?  41.980     ?     ?     ?     ?  ?           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
 1   1   9  0.648  0.197   0.356  
 2   2  11  0.971  0.111  -0.477  
 3   3   9  0.862  0.201   0.633  
 4   4   8  0.952  0.173   0.517  
 5   5   8  0.941  0.143   0.005  
 6   6   9  0.929  0.150  -0.266  
 7   7   9  0.948  0.111  -0.668  
 8   8   7  0.978  0.121  -0.353  
 9   9   8  0.973  0.131  -0.274  
10  10   5  0.986  0.123  -0.133  
11  11   6  0.977  0.082  -0.777  
12  12  14  0.922  0.157   0.575  
13  13   6  0.982  0.103  -0.526  
14  14   8  0.972  0.095  -0.758  
15  15   6  0.990  0.100  -0.394  
16  16  11  0.937  0.182   0.279  
17  17  11  0.974  0.131  -0.100  
18  18  12  0.979  0.091  -0.820  
19  19   7  0.970  0.115  -0.266  
20  20   5  0.984  0.101  -0.525  
21  21   9  0.965  0.169  -0.107  
22  22   7  0.963  0.099  -0.767  
23  23   7  0.965  0.096  -0.668  
24  24   5  0.956  0.111  -0.347  
25  25   7  0.958  0.083  -1.068  
26  26   8  0.968  0.099  -0.674  
27  27   9  0.944  0.146  -0.414  
28  28   8  0.977  0.099  -0.699  
29  29   4  0.972  0.097  -0.515  
30  30   7  0.982  0.103  -0.545  
31  31  12  0.971  0.115  -0.352  
32  32   7  0.968  0.094  -0.703  
33  33   7  0.962  0.099  -0.767  
34  34   9  0.968  0.163  -0.187  
35  35  11  0.979  0.101  -0.666  
36  36  12  0.979  0.095  -0.742  
37  37   8  0.961  0.108  -0.564  
38  38   4  0.955  0.090  -0.628  
39  39   7  0.984  0.094  -0.861  
40  40   7  0.983  0.129  -0.203  
41  41   9  0.960  0.099  -0.841  
42  42   7  0.955  0.117  -0.299  
43  43   7  0.964  0.117  -0.429  
44  44   9  0.945  0.158  -0.254  
45  45  10  0.918  0.155   0.291  
46  46   8  0.957  0.131  -0.267  
47  47  10  0.981  0.108  -0.481  
48  48   7  0.984  0.118  -0.410  
49  49   9  0.974  0.121  -0.748  
50  50   5  0.973  0.127  -0.062  
51  51  11  0.919  0.176   0.749  
52  52   5  0.698  0.271   2.251  
53  53   1  0.647  0.325       ?  
54  54   1  0.799  0.115       ?  
55  55   1  0.943  0.122       ?  
56  56   1  0.981  0.101       ?  
57  57   1  0.881  0.108       ?  
58  58   1  0.978  0.240       ?  
59  59   1  0.678  0.265       ?  
60  60   1  0.861  0.180       ?  
61  61   1  0.930  0.304       ?  
62  62   1  0.755  0.316       ?  
63  63   1  0.925  0.232       ?  
#
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  eds          2.35                                                                  Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
