data_2GPX

loop_
_pdbx_vrpt_database.id
_pdbx_vrpt_database.code
PDB  2GPX    
NDB  AD0062  
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    2GPX
_pdbx_vrpt_summary.PDB_deposition_date         2006-04-18
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2023-08-30
_pdbx_vrpt_summary.report_creation_date        2023-08-20:06:32
_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      "5'-D(*GP*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3'"  
2  non-polymer  "BARIUM 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  RSRZ_outliers_percent  
3  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   65.78  141614     ?     ?  
2  2  1   53.26    3665  1.60  1.60  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    3321  1.60  1.60  
5  1  3   68.17  130704     ?     ?  
6  2  3   39.28    3398  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  
#
_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      1.54
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       1.23
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   135
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  204
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       3.97
_pdbx_vrpt_summary_geometry.num_H_reduce     89
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   135
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.23
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  204
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.54
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 142.835
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            60.894
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         21.739
_pdbx_vrpt_summary_diffraction.I_over_sigma              4.39(1.60A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3137
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.339
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.401
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.475
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.309
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.963
_pdbx_vrpt_summary_diffraction.DCC_R                     0.18
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.22
_pdbx_vrpt_summary_diffraction.EDS_R                     0.19
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.60
_pdbx_vrpt_summary_diffraction.EDS_res_low               18.90
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[22.077,22.077,21.061,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.047
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 24.76 % 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 3.6024e-03."
_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         97.87
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      311
_pdbx_vrpt_summary_diffraction.percent_free_reflections  9.91
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.60
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        18.90
_pdbx_vrpt_summary_diffraction.PDB_R                     0.20
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.24
#
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_bond_outliers
_pdbx_vrpt_model_instance.count_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.count_mogul_bond_outliers
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
 1  1  1  A  1  DG   A    1  .  ?        1     1     ?     ?     ?  
 2  1  1  A  2  UMS  A    2  .  ?        ?     ?     ?     1     1  
 3  1  1  A  3  DG   A    3  .  ?        1     1     ?     ?     ?  
 4  1  1  A  4  BRU  A    4  .  ?        ?     ?     ?     3     4  
 5  1  1  A  5  DA   A    5  .  ?        ?     ?     ?     ?     ?  
 6  1  1  A  6  DC   A    6  .  ?        1     ?     ?     ?     ?  
 7  1  1  A  7  DA   A    7  .  ?        ?     ?     1     ?     ?  
 8  1  1  A  8  DC   A    8  .  ?        1     ?     1     ?     ?  
 9  1  2  B  .  BA   A  101  .  ?        ?     ?     ?     ?     ?  
10  1  3  C  .  HOH  A  102  .  ?        ?     ?     ?     ?     ?  
11  1  3  C  .  HOH  A  103  .  ?        ?     ?     ?     ?     ?  
12  1  3  C  .  HOH  A  104  .  ?        ?     ?     ?     ?     ?  
13  1  3  C  .  HOH  A  105  .  ?        ?     ?     ?     ?     ?  
14  1  3  C  .  HOH  A  106  .  ?        ?     ?     ?     ?     ?  
15  1  3  C  .  HOH  A  107  .  ?        ?     ?     ?     ?     ?  
16  1  3  C  .  HOH  A  108  .  ?        ?     ?     ?     ?     ?  
17  1  3  C  .  HOH  A  109  .  ?        ?     ?     ?     ?     ?  
18  1  3  C  .  HOH  A  110  .  ?        ?     ?     ?     ?     ?  
19  1  3  C  .  HOH  A  111  .  ?        ?     ?     ?     ?     ?  
20  1  3  C  .  HOH  A  112  .  ?        ?     ?     ?     ?     ?  
21  1  3  C  .  HOH  A  113  .  ?        ?     ?     ?     ?     ?  
22  1  3  C  .  HOH  A  114  .  ?        ?     ?     ?     ?     ?  
23  1  3  C  .  HOH  A  115  .  ?        ?     ?     ?     ?     ?  
24  1  3  C  .  HOH  A  116  .  ?        ?     ?     ?     ?     ?  
25  1  3  C  .  HOH  A  117  .  ?        ?     ?     ?     ?     ?  
26  1  3  C  .  HOH  A  118  .  ?        ?     ?     ?     ?     ?  
27  1  3  C  .  HOH  A  119  .  ?        ?     ?     ?     ?     ?  
28  1  3  C  .  HOH  A  120  .  ?        ?     ?     ?     ?     ?  
29  1  3  C  .  HOH  A  121  .  ?        ?     ?     ?     ?     ?  
30  1  3  C  .  HOH  A  122  .  ?        ?     ?     ?     ?     ?  
31  1  3  C  .  HOH  A  123  .  ?        ?     ?     ?     ?     ?  
32  1  3  C  .  HOH  A  124  .  ?        ?     ?     ?     ?     ?  
33  1  3  C  .  HOH  A  125  .  ?        ?     ?     ?     ?     ?  
34  1  3  C  .  HOH  A  126  .  ?        ?     ?     ?     ?     ?  
35  1  3  C  .  HOH  A  127  .  ?        ?     ?     ?     ?     ?  
36  1  3  C  .  HOH  A  128  .  ?        ?     ?     ?     ?     ?  
37  1  3  C  .  HOH  A  129  .  ?        ?     ?     ?     ?     ?  
38  1  3  C  .  HOH  A  130  .  ?        ?     ?     ?     ?     ?  
39  1  3  C  .  HOH  A  131  .  ?        ?     ?     ?     ?     ?  
40  1  3  C  .  HOH  A  132  .  ?        ?     ?     ?     ?     ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_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    12  21.250    21  1.43    31  2.32  molprobity  1.000  
 2   2    12  23.670    17  1.08    24  0.93  mogul       0.990  
 3   3    11  23.480    24  1.45    35  2.35  molprobity  1.000  
 4   4     9  22.450    18  2.28    26  1.59  mogul       0.993  
 5   5    11  21.080    24  0.57    37  0.87  molprobity  1.000  
 6   6    11  22.730    21  1.43    32  1.16  molprobity  1.000  
 7   7    11  22.610    24  0.60    37  0.99  molprobity  1.000  
 8   8    12  27.530    20  1.59    28  0.71  molprobity  1.000  
 9   9     ?  27.300     ?     ?     ?     ?  ?           0.880  
10  10     ?  20.260     ?     ?     ?     ?  ?           1.000  
11  11     ?  32.070     ?     ?     ?     ?  ?           1.000  
12  12     ?  35.460     ?     ?     ?     ?  ?           1.000  
13  13     ?  28.990     ?     ?     ?     ?  ?           1.000  
14  14     ?  25.510     ?     ?     ?     ?  ?           1.000  
15  15     ?  43.030     ?     ?     ?     ?  ?           1.000  
16  16     ?  29.240     ?     ?     ?     ?  ?           1.000  
17  17     ?  33.230     ?     ?     ?     ?  ?           1.000  
18  18     ?  29.110     ?     ?     ?     ?  ?           1.000  
19  19     ?  33.190     ?     ?     ?     ?  ?           1.000  
20  20     ?  39.030     ?     ?     ?     ?  ?           1.000  
21  21     ?  33.600     ?     ?     ?     ?  ?           1.000  
22  22     ?  37.130     ?     ?     ?     ?  ?           1.000  
23  23     ?  46.870     ?     ?     ?     ?  ?           1.000  
24  24     ?  28.950     ?     ?     ?     ?  ?           1.000  
25  25     ?  39.380     ?     ?     ?     ?  ?           1.000  
26  26     ?  26.340     ?     ?     ?     ?  ?           1.000  
27  27     ?  43.190     ?     ?     ?     ?  ?           1.000  
28  28     ?  42.820     ?     ?     ?     ?  ?           1.000  
29  29     ?  46.410     ?     ?     ?     ?  ?           1.000  
30  30     ?  51.320     ?     ?     ?     ?  ?           1.000  
31  31     ?  37.340     ?     ?     ?     ?  ?           1.000  
32  32     ?  47.570     ?     ?     ?     ?  ?           1.000  
33  33     ?  46.350     ?     ?     ?     ?  ?           1.000  
34  34     ?  52.580     ?     ?     ?     ?  ?           1.000  
35  35     ?  58.070     ?     ?     ?     ?  ?           1.000  
36  36     ?  51.120     ?     ?     ?     ?  ?           1.000  
37  37     ?  54.670     ?     ?     ?     ?  ?           1.000  
38  38     ?  63.610     ?     ?     ?     ?  ?           1.000  
39  39     ?  47.680     ?     ?     ?     ?  ?           1.000  
40  40     ?  61.870     ?     ?     ?     ?  ?           1.000  
#
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  7  "H2'"  1  0.43  2.52  
2  8  C6     1  0.43  2.52  
#
loop_
_pdbx_vrpt_instance_intra_bond_outliers.ordinal
_pdbx_vrpt_instance_intra_bond_outliers.instance_id
_pdbx_vrpt_instance_intra_bond_outliers.atom_1
_pdbx_vrpt_instance_intra_bond_outliers.atom_2
_pdbx_vrpt_instance_intra_bond_outliers.obs
_pdbx_vrpt_instance_intra_bond_outliers.mean
_pdbx_vrpt_instance_intra_bond_outliers.stdev
_pdbx_vrpt_instance_intra_bond_outliers.Z
1  1  C5  C6  1.474  1.419  0.010  5.47  
2  3  C5  C6  1.483  1.419  0.010  6.37  
3  6  C5  C6  1.387  1.339  0.008  5.97  
4  8  C5  C6  1.390  1.339  0.008  6.41  
#
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  1  "O4'"  "C1'"  N9  100.683  108.000  0.700  -10.45  
2  3  "O4'"  "C1'"  N9  100.404  108.000  0.700  -10.85  
#
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  2  C5  C4  1.50  1.43  952  0.02   3.02  0.00  
2  4  C4  C5  1.53  1.45   49  0.02   3.99  0.03  
3  4  C6  C5  1.41  1.34   57  0.02   3.45  0.04  
4  4  BR  C5  1.70  1.88  878  0.02  -7.55  0.03  
#
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  2  "O4'"  "C1'"  N1  101.25  108.36  1007  2.29  -3.11  0.17  
2  4  C6     C5     C4  116.26  120.67    41  1.02  -4.34  2.21  
3  4  BR     C5     C6  123.89  120.64    57  1.40   2.32  0.39  
4  4  "C2'"  "C1'"  N1  107.30  113.77   663  2.30  -2.81  0.61  
5  4  "O4'"  "C1'"  N1  100.94  107.86   804  1.79  -3.87  0.18  
#
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  19  0.936  0.082  -0.450  
 2   2  21  0.972  0.073       ?  
 3   3  22  0.860  0.113   0.141  
 4   4  20  0.971  0.085       ?  
 5   5  21  0.910  0.112  -0.060  
 6   6  19  0.903  0.113  -0.009  
 7   7  21  0.917  0.104  -0.177  
 8   8  19  0.919  0.100  -0.199  
 9   9   1  0.982  0.030       ?  
10  10   1  0.982  0.114       ?  
11  11   1  0.755  0.215       ?  
12  12   1  0.960  0.081       ?  
13  13   1  0.910  0.096       ?  
14  14   1  0.955  0.074       ?  
15  15   1  0.804  0.133       ?  
16  16   1  0.895  0.086       ?  
17  17   1  0.933  0.170       ?  
18  18   1  0.940  0.141       ?  
19  19   1  0.891  0.097       ?  
20  20   1  0.690  0.355       ?  
21  21   1  0.873  0.127       ?  
22  22   1  0.820  0.104       ?  
23  23   1  0.677  0.188       ?  
24  24   1  0.931  0.125       ?  
25  25   1  0.736  0.231       ?  
26  26   1  0.978  0.059       ?  
27  27   1  0.771  0.208       ?  
28  28   1  0.869  0.254       ?  
29  29   1  0.682  0.112       ?  
30  30   1  0.674  0.148       ?  
31  31   1  0.831  0.129       ?  
32  32   1  0.809  0.186       ?  
33  33   1  0.737  0.448       ?  
34  34   1  0.718  0.280       ?  
35  35   1  0.891  0.126       ?  
36  36   1  0.572  0.096       ?  
37  37   1  0.779  0.137       ?  
38  38   1  0.550  0.159       ?  
39  39   1  0.788  0.271       ?  
40  40   1  0.838  0.125       ?  
#
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        "1.8.5 (274361), CSD as541be (2020)"                                  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  
##
