data_2KNL

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  2KNL
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   nmr
#
_pdbx_vrpt_summary.entry_id                    2KNL
_pdbx_vrpt_summary.PDB_deposition_date         2009-08-26
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2022-03-16
_pdbx_vrpt_summary.report_creation_date        2022-03-07:02:09
_pdbx_vrpt_summary.attempted_validation_steps  mogul,molprobity,validation-pack,coreclust,chemicalshifts,percentiles,writepdf,writexml,writecif
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "DNA (5'-D(*TP*CP*CP*GP*CP*GP*GP*A)-3')"  
2  non-polymer  PROPANE  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  pdb    
2  nmr  x-ray  
#
_pdbx_vrpt_percentile_type.id    1
_pdbx_vrpt_percentile_type.type  all_atom_clashscore
#
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   99.94  158937  ?     ?     
2  2  1  100.00   12864  ?     ?     
#
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  2.43  1.58   180   276  
2  1  1  B  B  2.35  1.55   180   276  
3  1  2  C  A     ?     ?     ?     ?  
#
_pdbx_vrpt_summary_geometry.ordinal                 1
_pdbx_vrpt_summary_geometry.clashscore_full_length  0.00
_pdbx_vrpt_summary_geometry.num_H_reduce            186
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ          360
_pdbx_vrpt_summary_geometry.bonds_RMSZ              1.56
_pdbx_vrpt_summary_geometry.num_angles_RMSZ         552
_pdbx_vrpt_summary_geometry.angles_RMSZ             2.39
#
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_plane_outliers
 1  1  1  A  1  DT   A   1  .  ?        2     ?  
 2  1  1  A  2  DC   A   2  .  ?        2     1  
 3  1  1  A  3  DC   A   3  .  ?        2     1  
 4  1  1  A  4  DG   A   4  .  ?        2     ?  
 5  1  1  A  5  DC   A   5  .  ?        2     ?  
 6  1  1  A  6  DG   A   6  .  ?        1     ?  
 7  1  1  A  7  DG   A   7  .  ?        1     ?  
 8  1  1  A  8  DA   A   8  .  ?        3     ?  
 9  1  1  B  1  DT   B   9  .  ?        2     ?  
10  1  1  B  2  DC   B  10  .  ?        2     1  
11  1  1  B  3  DC   B  11  .  ?        2     1  
12  1  1  B  4  DG   B  12  .  ?        1     1  
13  1  1  B  5  DC   B  13  .  ?        2     ?  
14  1  1  B  6  DG   B  14  .  ?        1     ?  
15  1  1  B  7  DG   B  15  .  ?        1     ?  
16  1  1  B  8  DA   B  16  .  ?        3     ?  
17  1  2  C  .  TME  A  17  .  ?        ?     ?  
#
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.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  13  19  1.75  30  2.41  molprobity  
 2   2  11  21  1.52  32  2.47  molprobity  
 3   3  11  21  1.50  32  2.32  molprobity  
 4   4  10  25  1.70  39  2.69  molprobity  
 5   5  11  21  1.57  32  2.59  molprobity  
 6   6  11  25  1.48  39  2.12  molprobity  
 7   7  11  25  1.57  39  2.04  molprobity  
 8   8  12  23  1.53  33  2.79  molprobity  
 9   9  13  19  1.75  30  2.49  molprobity  
10  10  11  21  1.49  32  2.50  molprobity  
11  11  11  21  1.52  32  2.38  molprobity  
12  12  10  25  1.49  39  2.15  molprobity  
13  13  11  21  1.57  32  2.50  molprobity  
14  14  11  25  1.48  39  1.99  molprobity  
15  15  11  25  1.58  39  2.05  molprobity  
16  16  12  23  1.52  33  2.77  molprobity  
17  17   6   2  0.71   0     ?  mogul       
#
loop_
_pdbx_vrpt_instance_intra_plane_outliers.ordinal
_pdbx_vrpt_instance_intra_plane_outliers.instance_id
_pdbx_vrpt_instance_intra_plane_outliers.type
_pdbx_vrpt_instance_intra_plane_outliers.plane_rmsd
1   2  sidechain  0.07  
2   3  sidechain  0.07  
3  10  sidechain  0.06  
4  11  sidechain  0.08  
5  12  sidechain  0.08  
#
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
_pdbx_vrpt_instance_intra_angle_outliers.link
 1   1  C6     C5     C7     119.248  122.900  0.600  -6.09  ?     
 2   1  N3     C2     O2     119.081  122.300  0.600  -5.36  ?     
 3   2  N1     C2     O2     122.696  118.900  0.600   6.33  ?     
 4   2  N3     C2     O2     116.698  121.900  0.700  -7.43  ?     
 5   3  N1     C2     O2     122.299  118.900  0.600   5.67  ?     
 6   3  N3     C2     O2     116.853  121.900  0.700  -7.21  ?     
 7   4  P      "O3'"  "C3'"  126.680  119.700  1.200   5.82  Y     
 8   4  N3     C2     N2     123.716  119.900  0.700   5.45  ?     
 9   5  N1     C2     O2     121.946  118.900  0.600   5.08  ?     
10   5  N3     C2     O2     116.487  121.900  0.700  -7.73  ?     
11   6  "O4'"  "C4'"  "C3'"  109.607  106.000  0.600   6.01  ?     
12   7  "O4'"  "C4'"  "C3'"  109.169  106.000  0.600   5.28  ?     
13   8  C4     C5     C6     113.624  117.000  0.500  -6.75  ?     
14   8  C5     C6     N1     121.211  117.700  0.500   7.02  ?     
15   8  N1     C6     N6     113.416  118.600  0.600  -8.64  ?     
16   9  C6     C5     C7     119.018  122.900  0.600  -6.47  ?     
17   9  N3     C2     O2     119.022  122.300  0.600  -5.46  ?     
18  10  N1     C2     O2     122.688  118.900  0.600   6.31  ?     
19  10  N3     C2     O2     116.609  121.900  0.700  -7.56  ?     
20  11  N1     C2     O2     122.442  118.900  0.600   5.90  ?     
21  11  N3     C2     O2     116.751  121.900  0.700  -7.36  ?     
22  12  N1     C6     O6     116.759  119.900  0.600  -5.23  ?     
23  13  N1     C2     O2     122.248  118.900  0.600   5.58  ?     
24  13  N3     C2     O2     116.494  121.900  0.700  -7.72  ?     
25  14  "O4'"  "C4'"  "C3'"  109.343  106.000  0.600   5.57  ?     
26  15  "O4'"  "C4'"  "C3'"  109.299  106.000  0.600   5.50  ?     
27  16  C4     C5     C6     113.573  117.000  0.500  -6.86  ?     
28  16  C5     C6     N1     121.243  117.700  0.500   7.09  ?     
29  16  N1     C6     N6     113.560  118.600  0.600  -8.40  ?     
#
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  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
