data_6Y14

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.067
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6Y14
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6Y14
_pdbx_vrpt_summary.PDB_deposition_date         2020-02-11
_pdbx_vrpt_summary.PDB_revision_number         6
_pdbx_vrpt_summary.PDB_revision_date           2024-10-23
_pdbx_vrpt_summary.report_creation_date        2024-11-26:00:31
_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      bp65  
2  non-polymer  "CITRIC ACID"  
3  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  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  0.9  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   99.93    1367  0.80  1.00  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1294  0.80  1.00  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1295  0.80  1.00  
 7  1  4    4.13  164620     ?     ?  
 8  2  4    3.01    1231  0.80  1.00  
 9  1  5    8.18  164625     ?     ?  
10  2  5    0.36    1232  0.80  1.00  
#
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    4.13  
 6  8  4  A  1  1  A    3.01  
 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  100.00  
10  6  3  B  1  1  B  100.00  
11  7  4  B  1  1  B    4.13  
12  8  4  B  1  1  B    3.01  
#
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  0.74  0.66  84  109  
2  1  1  B  B  0.81  0.93  84  109  
#
_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                   220
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 168
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.81
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                218
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.78
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            43.660
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.474
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.836
_pdbx_vrpt_summary_diffraction.DCC_R                     0.2764
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.2929
_pdbx_vrpt_summary_diffraction.EDS_R                     0.2953
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.00
_pdbx_vrpt_summary_diffraction.EDS_res_low               27.65
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.data_completeness         74.33
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      1092
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.90
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     18.18
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       0.90
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        27.70
_pdbx_vrpt_summary_diffraction.PDB_R                     0.1913
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.11
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.004 (Gargrove)"
_pdbx_vrpt_summary_diffraction.EDS_R_warning             "The R factor obtained from EDS is 0.2953, which does not match the depositor's R factor of 0.1264. Please interpret the results in this section carefully."
#
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_mogul_bond_outliers
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
 1  1  1  A   1  O65  A  101  .  ?        ?     ?  
 2  1  1  A   2  LYS  A  102  .  ?        ?     ?  
 3  1  1  A   3  LYS  A  103  .  ?        ?     ?  
 4  1  1  A   4  LEU  A  104  .  ?        ?     ?  
 5  1  1  A   5  LEU  A  105  .  ?        ?     ?  
 6  1  1  A   6  LYS  A  106  .  ?        ?     ?  
 7  1  1  A   7  CYS  A  107  .  ?        ?     ?  
 8  1  1  A   8  LEU  A  108  .  ?        ?     ?  
 9  1  1  A   9  LYS  A  109  .  ?        ?     ?  
10  1  1  A  10  CYS  A  110  .  ?        ?     ?  
11  1  1  A  11  LEU  A  111  .  ?        ?     ?  
12  1  1  A  12  LEU  A  112  .  ?        ?     ?  
13  1  1  A  13  NH2  A  113  .  ?        ?     ?  
14  1  1  B   1  O65  B  101  .  ?        ?     ?  
15  1  1  B   2  LYS  B  102  .  ?        ?     ?  
16  1  1  B   3  LYS  B  103  .  ?        ?     ?  
17  1  1  B   4  LEU  B  104  .  ?        ?     ?  
18  1  1  B   5  LEU  B  105  .  ?        ?     ?  
19  1  1  B   6  LYS  B  106  .  ?        ?     ?  
20  1  1  B   7  CYS  B  107  .  ?        ?     ?  
21  1  1  B   8  LEU  B  108  .  ?        ?     ?  
22  1  1  B   9  LYS  B  109  .  ?        ?     ?  
23  1  1  B  10  CYS  B  110  .  ?        ?     ?  
24  1  1  B  11  LEU  B  111  .  ?        ?     ?  
25  1  1  B  12  LEU  B  112  .  ?        ?     ?  
26  1  1  B  13  NH2  B  113  .  ?        ?     ?  
27  1  2  C   .  CIT  A  201  .  ?        2     3  
28  1  2  D   .  CIT  B  201  .  ?        3     7  
29  1  3  E   .  HOH  A  301  .  ?        ?     ?  
30  1  3  E   .  HOH  A  302  .  ?        ?     ?  
31  1  3  E   .  HOH  A  303  .  ?        ?     ?  
32  1  3  E   .  HOH  A  304  .  ?        ?     ?  
33  1  3  E   .  HOH  A  305  .  ?        ?     ?  
34  1  3  E   .  HOH  A  306  .  ?        ?     ?  
35  1  3  E   .  HOH  A  307  .  ?        ?     ?  
36  1  3  E   .  HOH  A  308  .  ?        ?     ?  
37  1  3  F   .  HOH  B  301  .  ?        ?     ?  
38  1  3  F   .  HOH  B  302  .  ?        ?     ?  
39  1  3  F   .  HOH  B  303  .  ?        ?     ?  
40  1  3  F   .  HOH  B  304  .  ?        ?     ?  
41  1  3  F   .  HOH  B  305  .  ?        ?     ?  
#
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  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
 2   2  mtmt       ?      ?  ?          12  3.950     9  0.61    11  1.16  molprobity  1.000  
 3   3  mttt  -144.6  161.4  Favored    13  3.950     9  0.36    11  0.93  molprobity  1.000  
 4   4  mt     -69.0  -46.2  Favored    11  3.950     8  0.90    11  0.58  molprobity  1.000  
 5   5  mt     -67.4  -37.6  Favored    11  3.950     8  0.49    11  0.89  molprobity  1.000  
 6   6  mttt   -59.5  -39.9  Favored    13  3.950     9  0.38    11  0.62  molprobity  1.000  
 7   7  t      -61.9  -47.0  Favored     4  3.950     6  0.71     8  0.37  molprobity  1.000  
 8   8  mt     -57.6  -45.0  Favored    11  3.950     8  0.85    11  0.40  molprobity  1.000  
 9   9  ?      -63.9  -41.5  Favored     4  3.950     6  0.96     8  0.75  molprobity  1.000  
10  10  t      -66.1  -42.5  Favored     4  3.950     6  0.50     8  0.90  molprobity  1.000  
11  11  mt     -68.7  -42.2  Favored    11  3.950     8  0.44    11  0.49  molprobity  1.000  
12  12  mt     -80.9  142.8  Favored    11  3.950     7  0.87     8  0.50  molprobity  1.000  
13  13  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
14  14  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
15  15  mtmt       ?      ?  ?          12  3.950     9  1.13    11  0.72  molprobity  1.000  
16  16  mttt  -122.9  153.7  Favored    13  3.950     9  0.83    11  0.72  molprobity  1.000  
17  17  tp     -65.6  -46.2  Favored    11  3.950     8  0.50    11  0.81  molprobity  1.000  
18  18  mt     -69.0  -35.6  Favored    11  3.950     8  0.55    11  1.27  molprobity  1.000  
19  19  mtpp   -60.4  -39.7  Favored    13  3.950     9  0.59    11  0.74  molprobity  1.000  
20  20  t      -61.7  -46.7  Favored     4  3.950     6  0.73     8  0.38  molprobity  1.000  
21  21  mt     -55.9  -47.8  Favored    11  3.950     8  0.40    11  1.08  molprobity  1.000  
22  22  ?      -63.1  -39.7  Favored     4  3.950     6  1.68     8  0.50  molprobity  1.000  
23  23  t      -68.2  -40.0  Favored     4  3.950     6  1.21     8  0.65  molprobity  1.000  
24  24  mt     -70.8  -41.9  Favored    11  3.950     8  0.51    11  0.68  molprobity  1.000  
25  25  mt     -86.0  147.4  Favored    11  3.950     7  1.44     8  0.81  molprobity  1.000  
26  26  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
27  27  ?          ?      ?  ?           5  3.950    12  1.66    17  1.73  mogul       1.000  
28  28  ?          ?      ?  ?           5  3.950    12  2.08    17  1.81  mogul       1.000  
29  29  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
30  30  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
31  31  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
32  32  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
33  33  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
34  34  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
35  35  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
36  36  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
37  37  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
38  38  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
39  39  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
40  40  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
41  41  ?          ?      ?  ?           ?  3.950     ?     ?     ?     ?  ?           1.000  
#
loop_
_pdbx_vrpt_instance_mogul_bond_outliers.ordinal
_pdbx_vrpt_instance_mogul_bond_outliers.instance_id
_pdbx_vrpt_instance_mogul_bond_outliers.atom_1
_pdbx_vrpt_instance_mogul_bond_outliers.atom_2
_pdbx_vrpt_instance_mogul_bond_outliers.obsval
_pdbx_vrpt_instance_mogul_bond_outliers.mean
_pdbx_vrpt_instance_mogul_bond_outliers.numobs
_pdbx_vrpt_instance_mogul_bond_outliers.stdev
_pdbx_vrpt_instance_mogul_bond_outliers.Zscore
_pdbx_vrpt_instance_mogul_bond_outliers.mindiff
1  27  C4  C3  1.51  1.54    385  0.01  -2.18  0.00  
2  27  C3  C6  1.57  1.53     80  0.01   4.09  0.01  
3  28  O2  C1  1.21  1.30  10681  0.03  -2.77  0.00  
4  28  C2  C3  1.58  1.54    385  0.01   3.38  0.00  
5  28  C4  C3  1.59  1.54    385  0.01   4.48  0.02  
#
loop_
_pdbx_vrpt_instance_mogul_angle_outliers.ordinal
_pdbx_vrpt_instance_mogul_angle_outliers.instance_id
_pdbx_vrpt_instance_mogul_angle_outliers.atom_1
_pdbx_vrpt_instance_mogul_angle_outliers.atom_2
_pdbx_vrpt_instance_mogul_angle_outliers.atom_3
_pdbx_vrpt_instance_mogul_angle_outliers.obsval
_pdbx_vrpt_instance_mogul_angle_outliers.mean
_pdbx_vrpt_instance_mogul_angle_outliers.numobs
_pdbx_vrpt_instance_mogul_angle_outliers.stdev
_pdbx_vrpt_instance_mogul_angle_outliers.Zscore
_pdbx_vrpt_instance_mogul_angle_outliers.mindiff
 1  27  O1  C1  C2  116.90  122.95  1020  2.83  -2.14  0.07  
 2  27  C2  C3  C6  104.78  110.03   122  2.21  -2.37  0.03  
 3  27  O7  C3  C6  101.46  108.96    70  1.42  -5.29  4.47  
 4  28  O1  C1  C2  114.77  122.95  1020  2.83  -2.89  0.02  
 5  28  O2  C1  C2  121.44  114.35  1020  3.17   2.24  0.03  
 6  28  C2  C3  C6  105.30  110.03   122  2.21  -2.14  0.09  
 7  28  O7  C3  C6  105.04  108.96    70  1.42  -2.76  0.89  
 8  28  C3  C4  C5  106.40  113.92   225  2.73  -2.75  1.67  
 9  28  O5  C6  C3  128.35  122.09    80  1.94   3.23  2.58  
10  28  O6  C6  C3  108.60  113.14    80  1.92  -2.36  2.07  
#
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  20  0.880  0.112      ?  0.623   18.180  
 2   2  22  0.896  0.107  0.688  0.511    0.000  
 3   3  22  0.909  0.091  0.239  0.608    0.000  
 4   4  19  0.953  0.086  1.421  0.686   12.500  
 5   5  19  0.876  0.154  4.315  0.437    0.000  
 6   6  22  0.916  0.097  0.407  0.637    0.000  
 7   7  10  0.981  0.061  0.902  0.653   16.670  
 8   8  19  0.921  0.096  1.847  0.623   25.000  
 9   9  10  0.938  0.100  0.492  0.556   16.670  
10  10  10  0.989  0.054  0.591  0.594   33.330  
11  11  19  0.926  0.090  1.591  0.588    0.000  
12  12  19  0.876  0.108  2.357  0.647    0.000  
13  13   3  0.921  0.091      ?  0.789    0.000  
14  14  20  0.909  0.091      ?  0.646    0.000  
15  15  22  0.857  0.144  1.728  0.553   11.110  
16  16  22  0.890  0.119  1.025  0.663   11.110  
17  17  19  0.949  0.094  1.762  0.540    0.000  
18  18  19  0.930  0.118  2.783  0.619   12.500  
19  19  22  0.928  0.126  1.222  0.580   22.220  
20  20  10  0.982  0.057  0.724  0.606   16.670  
21  21  19  0.910  0.147  4.017  0.508   12.500  
22  22  10  0.947  0.132  1.390  0.293   50.000  
23  23  10  0.986  0.057  0.724  0.758   50.000  
24  24  19  0.946  0.071  0.783  0.627    0.000  
25  25  19  0.924  0.088  1.506  0.660    0.000  
26  26   3  0.964  0.074      ?  0.854  100.000  
27  27  18  0.870  0.092      ?  0.575   23.080  
28  28  18  0.884  0.085      ?  0.580   15.380  
29  29   1  0.933  0.088      ?  0.942  100.000  
30  30   1  0.852  0.147      ?  0.810  100.000  
31  31   1  0.951  0.197      ?  0.535    0.000  
32  32   1  0.907  0.102      ?  0.800  100.000  
33  33   1  0.974  0.046      ?  0.706    0.000  
34  34   1  0.959  0.086      ?  0.823  100.000  
35  35   1  0.906  0.131      ?  0.490    0.000  
36  36   1  0.954  0.047      ?  0.682    0.000  
37  37   1  0.915  0.087      ?  0.683    0.000  
38  38   1  0.939  0.081      ?  0.674    0.000  
39  39   1  0.848  0.220      ?  0.431    0.000  
40  40   1  0.915  0.083      ?  0.767    0.000  
41  41   1  0.880  0.106      ?  0.752    0.000  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  mogul        "2022.3.0, CSD as543be (2022)"                                        Y  
3  eds          3.0                                                                   Y  
4  dcc          '"2.29  (2024-07-11))"'                                               Y  
5  xtriage      1.21                                                                  N  
6  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
