data_2DLJ

loop_
_pdbx_vrpt_database.id
_pdbx_vrpt_database.code
PDB  2DLJ    
NDB  AD0063  
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    2DLJ
_pdbx_vrpt_summary.PDB_deposition_date         2006-04-19
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-02-14
_pdbx_vrpt_summary.report_creation_date        2024-02-07:02:45
_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  water    water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.5  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore    
2  RSRZ_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   99.96  141614     ?     ?  
2  2  1   99.94    3144  1.50  1.50  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    2884  1.50  1.50  
#
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      1.49
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       1.19
_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       0.00
_pdbx_vrpt_summary_geometry.num_H_reduce     89
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   135
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.19
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  204
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.49
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 107.028
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            45.014
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         15.168
_pdbx_vrpt_summary_diffraction.I_over_sigma              8.32(1.50A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3753
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.259
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.354
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.488
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.322
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.966
_pdbx_vrpt_summary_diffraction.DCC_R                     0.17
_pdbx_vrpt_summary_diffraction.EDS_R                     0.18
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.50
_pdbx_vrpt_summary_diffraction.EDS_res_low               18.61
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[14.865,14.865,15.812,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.062
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 20.13 % 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 9.2915e-03. 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         0
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         98.64
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      0
_pdbx_vrpt_summary_diffraction.percent_free_reflections  0.00
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.50
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        18.61
_pdbx_vrpt_summary_diffraction.PDB_R                     0.17
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.22
#
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_plane_outliers
_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     ?     ?     ?  
 4  1  1  A  4  BRU  A   4  .  ?        ?     ?     ?     2     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  .  ?        ?     ?     ?     ?     ?  
 8  1  1  A  8  DC   A   8  .  ?        ?     ?     1     ?     ?  
 9  1  2  B  .  HOH  A   9  .  ?        ?     ?     ?     ?     ?  
10  1  2  B  .  HOH  A  10  .  ?        ?     ?     ?     ?     ?  
11  1  2  B  .  HOH  A  11  .  ?        ?     ?     ?     ?     ?  
12  1  2  B  .  HOH  A  12  .  ?        ?     ?     ?     ?     ?  
13  1  2  B  .  HOH  A  13  .  ?        ?     ?     ?     ?     ?  
14  1  2  B  .  HOH  A  14  .  ?        ?     ?     ?     ?     ?  
15  1  2  B  .  HOH  A  15  .  ?        ?     ?     ?     ?     ?  
16  1  2  B  .  HOH  A  16  .  ?        ?     ?     ?     ?     ?  
17  1  2  B  .  HOH  A  17  .  ?        ?     ?     ?     ?     ?  
18  1  2  B  .  HOH  A  18  .  ?        ?     ?     ?     ?     ?  
19  1  2  B  .  HOH  A  19  .  ?        ?     ?     ?     ?     ?  
20  1  2  B  .  HOH  A  20  .  ?        ?     ?     ?     ?     ?  
21  1  2  B  .  HOH  A  21  .  ?        ?     ?     ?     ?     ?  
22  1  2  B  .  HOH  A  22  .  ?        ?     ?     ?     ?     ?  
23  1  2  B  .  HOH  A  23  .  ?        ?     ?     ?     ?     ?  
24  1  2  B  .  HOH  A  24  .  ?        ?     ?     ?     ?     ?  
25  1  2  B  .  HOH  A  25  .  ?        ?     ?     ?     ?     ?  
26  1  2  B  .  HOH  A  26  .  ?        ?     ?     ?     ?     ?  
27  1  2  B  .  HOH  A  27  .  ?        ?     ?     ?     ?     ?  
28  1  2  B  .  HOH  A  28  .  ?        ?     ?     ?     ?     ?  
29  1  2  B  .  HOH  A  29  .  ?        ?     ?     ?     ?     ?  
30  1  2  B  .  HOH  A  30  .  ?        ?     ?     ?     ?     ?  
31  1  2  B  .  HOH  A  31  .  ?        ?     ?     ?     ?     ?  
32  1  2  B  .  HOH  A  32  .  ?        ?     ?     ?     ?     ?  
33  1  2  B  .  HOH  A  33  .  ?        ?     ?     ?     ?     ?  
34  1  2  B  .  HOH  A  34  .  ?        ?     ?     ?     ?     ?  
35  1  2  B  .  HOH  A  35  .  ?        ?     ?     ?     ?     ?  
36  1  2  B  .  HOH  A  36  .  ?        ?     ?     ?     ?     ?  
37  1  2  B  .  HOH  A  37  .  ?        ?     ?     ?     ?     ?  
38  1  2  B  .  HOH  A  38  .  ?        ?     ?     ?     ?     ?  
39  1  2  B  .  HOH  A  39  .  ?        ?     ?     ?     ?     ?  
40  1  2  B  .  HOH  A  40  .  ?        ?     ?     ?     ?     ?  
41  1  2  B  .  HOH  A  41  .  ?        ?     ?     ?     ?     ?  
42  1  2  B  .  HOH  A  42  .  ?        ?     ?     ?     ?     ?  
43  1  2  B  .  HOH  A  43  .  ?        ?     ?     ?     ?     ?  
44  1  2  B  .  HOH  A  44  .  ?        ?     ?     ?     ?     ?  
45  1  2  B  .  HOH  A  45  .  ?        ?     ?     ?     ?     ?  
46  1  2  B  .  HOH  A  46  .  ?        ?     ?     ?     ?     ?  
47  1  2  B  .  HOH  A  47  .  ?        ?     ?     ?     ?     ?  
48  1  2  B  .  HOH  A  48  .  ?        ?     ?     ?     ?     ?  
49  1  2  B  .  HOH  A  49  .  ?        ?     ?     ?     ?     ?  
50  1  2  B  .  HOH  A  50  .  ?        ?     ?     ?     ?     ?  
51  1  2  B  .  HOH  A  51  .  ?        ?     ?     ?     ?     ?  
52  1  2  B  .  HOH  A  52  .  ?        ?     ?     ?     ?     ?  
53  1  2  B  .  HOH  A  53  .  ?        ?     ?     ?     ?     ?  
#
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  14.950    21  1.39    31  2.23  molprobity  1.000  
 2   2    12  15.680    17  1.13    24  1.03  mogul       0.993  
 3   3    11  17.180    24  1.32    35  2.19  molprobity  1.000  
 4   4     9  16.140    18  2.50    26  1.30  mogul       0.962  
 5   5    11  13.560    24  0.64    37  0.68  molprobity  1.000  
 6   6    11  13.460    21  1.54    32  1.33  molprobity  1.000  
 7   7    11  14.150    24  0.88    37  0.96  molprobity  1.000  
 8   8    12  17.150    20  1.22    28  0.87  molprobity  1.000  
 9   9     ?  14.590     ?     ?     ?     ?  ?           1.000  
10  10     ?  23.780     ?     ?     ?     ?  ?           1.000  
11  11     ?  22.330     ?     ?     ?     ?  ?           1.000  
12  12     ?  20.450     ?     ?     ?     ?  ?           1.000  
13  13     ?  25.080     ?     ?     ?     ?  ?           1.000  
14  14     ?  24.330     ?     ?     ?     ?  ?           1.000  
15  15     ?  19.710     ?     ?     ?     ?  ?           1.000  
16  16     ?  23.020     ?     ?     ?     ?  ?           1.000  
17  17     ?  17.270     ?     ?     ?     ?  ?           1.000  
18  18     ?  25.930     ?     ?     ?     ?  ?           1.000  
19  19     ?  28.010     ?     ?     ?     ?  ?           1.000  
20  20     ?  23.580     ?     ?     ?     ?  ?           1.000  
21  21     ?  25.160     ?     ?     ?     ?  ?           1.000  
22  22     ?  28.150     ?     ?     ?     ?  ?           1.000  
23  23     ?  27.430     ?     ?     ?     ?  ?           1.000  
24  24     ?  29.880     ?     ?     ?     ?  ?           1.000  
25  25     ?  32.240     ?     ?     ?     ?  ?           1.000  
26  26     ?  23.200     ?     ?     ?     ?  ?           1.000  
27  27     ?  27.880     ?     ?     ?     ?  ?           1.000  
28  28     ?  23.010     ?     ?     ?     ?  ?           1.000  
29  29     ?  27.980     ?     ?     ?     ?  ?           1.000  
30  30     ?  29.000     ?     ?     ?     ?  ?           1.000  
31  31     ?  19.890     ?     ?     ?     ?  ?           1.000  
32  32     ?  29.870     ?     ?     ?     ?  ?           1.000  
33  33     ?  36.570     ?     ?     ?     ?  ?           1.000  
34  34     ?  26.290     ?     ?     ?     ?  ?           1.000  
35  35     ?  30.760     ?     ?     ?     ?  ?           1.000  
36  36     ?  31.170     ?     ?     ?     ?  ?           1.000  
37  37     ?  27.920     ?     ?     ?     ?  ?           1.000  
38  38     ?  35.040     ?     ?     ?     ?  ?           1.000  
39  39     ?  38.660     ?     ?     ?     ?  ?           1.000  
40  40     ?  35.670     ?     ?     ?     ?  ?           1.000  
41  41     ?  33.020     ?     ?     ?     ?  ?           1.000  
42  42     ?  46.000     ?     ?     ?     ?  ?           1.000  
43  43     ?  35.700     ?     ?     ?     ?  ?           1.000  
44  44     ?  50.530     ?     ?     ?     ?  ?           1.000  
45  45     ?  48.050     ?     ?     ?     ?  ?           1.000  
46  46     ?  49.780     ?     ?     ?     ?  ?           1.000  
47  47     ?  33.620     ?     ?     ?     ?  ?           1.000  
48  48     ?  36.320     ?     ?     ?     ?  ?           1.000  
49  49     ?  45.210     ?     ?     ?     ?  ?           1.000  
50  50     ?  42.650     ?     ?     ?     ?  ?           1.000  
51  51     ?  46.430     ?     ?     ?     ?  ?           1.000  
52  52     ?  47.150     ?     ?     ?     ?  ?           1.000  
53  53     ?  54.940     ?     ?     ?     ?  ?           1.000  
#
_pdbx_vrpt_instance_intra_plane_outliers.ordinal      1
_pdbx_vrpt_instance_intra_plane_outliers.instance_id  8
_pdbx_vrpt_instance_intra_plane_outliers.type         sidechain
_pdbx_vrpt_instance_intra_plane_outliers.plane_rmsd   0.07
#
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  1.473  1.419  0.010  5.40  
2  6  C5  C6  1.389  1.339  0.008  6.21  
#
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  100.501  108.000  0.700  -10.71  
2  3  "O4'"  "C1'"  N9  101.249  108.000  0.700   -9.64  
#
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   3.24  0.00  
2  4  C6  C5  1.39  1.34   57  0.02   2.40  0.02  
3  4  BR  C5  1.65  1.88  878  0.02  -9.83  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  101.75  108.36  1007  2.29  -2.90  0.15  
2  4  C6     C5     C4  118.24  120.67    41  1.02  -2.40  0.23  
3  4  BR     C5     C6  123.72  120.64    57  1.40   2.20  0.22  
4  4  "C2'"  "C1'"  N1  108.21  113.77   663  2.30  -2.41  0.30  
5  4  "O4'"  "C1'"  N1  100.67  107.86   804  1.79  -4.02  0.33  
#
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  0.959  0.068  -0.569  
 2   2  21  0.985  0.057       ?  
 3   3  22  0.903  0.097  -0.008  
 4   4  20  0.950  0.079       ?  
 5   5  21  0.953  0.088  -0.227  
 6   6  19  0.963  0.074  -0.502  
 7   7  21  0.946  0.082  -0.314  
 8   8  19  0.960  0.071  -0.550  
 9   9   1  0.990  0.180       ?  
10  10   1  0.969  0.068       ?  
11  11   1  0.984  0.042       ?  
12  12   1  0.990  0.166       ?  
13  13   1  0.870  0.093       ?  
14  14   1  0.855  0.118       ?  
15  15   1  0.975  0.050       ?  
16  16   1  0.960  0.100       ?  
17  17   1  0.987  0.073       ?  
18  18   1  0.978  0.179       ?  
19  19   1  0.972  0.098       ?  
20  20   1  0.939  0.112       ?  
21  21   1  0.918  0.151       ?  
22  22   1  0.890  0.183       ?  
23  23   1  0.951  0.210       ?  
24  24   1  0.952  0.277       ?  
25  25   1  0.921  0.168       ?  
26  26   1  0.946  0.131       ?  
27  27   1  0.958  0.105       ?  
28  28   1  0.945  0.062       ?  
29  29   1  0.928  0.427       ?  
30  30   1  0.906  0.100       ?  
31  31   1  0.929  0.091       ?  
32  32   1  0.963  0.159       ?  
33  33   1  0.932  0.119       ?  
34  34   1  0.873  0.120       ?  
35  35   1  0.922  0.164       ?  
36  36   1  0.838  0.099       ?  
37  37   1  0.973  0.181       ?  
38  38   1  0.943  0.081       ?  
39  39   1  0.777  0.163       ?  
40  40   1  0.880  0.237       ?  
41  41   1  0.933  0.309       ?  
42  42   1  0.570  0.291       ?  
43  43   1  0.885  0.298       ?  
44  44   1  0.366  0.280       ?  
45  45   1  0.763  0.300       ?  
46  46   1  0.707  0.154       ?  
47  47   1  0.942  0.373       ?  
48  48   1  0.908  0.293       ?  
49  49   1  0.789  0.213       ?  
50  50   1  0.903  0.135       ?  
51  51   1  0.720  0.296       ?  
52  52   1  0.766  0.125       ?  
53  53   1  0.712  0.176       ?  
#
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          2.36                                                                  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  
##
