- PDB-6tpx: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-((1-acetylpiperidin-4... -
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Basic information
Entry
Database: PDB / ID: 6tpx
Title
N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-((1-acetylpiperidin-4-yl)methyl)-2-(4-hydroxy-3,5-dimethylphenyl)-N-methyl-1H-benzo[d]imidazole-5-carboxamide
Method to determine structure: MOLECULAR REPLACEMENT Starting model: non published structure Resolution: 1.48→37.218 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.365 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.075 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1814
978
5.155 %
Rwork
0.1552
-
-
all
0.156
-
-
obs
-
18971
95.471 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Biso mean: 19.439 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.047 Å2
-0 Å2
0 Å2
2-
-
0.195 Å2
-0 Å2
3-
-
-
-1.242 Å2
Refinement step
Cycle: LAST / Resolution: 1.48→37.218 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1061
0
44
214
1319
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.004
0.013
1148
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
1048
X-RAY DIFFRACTION
r_angle_refined_deg
1.222
1.711
1562
X-RAY DIFFRACTION
r_angle_other_deg
1.283
1.609
2461
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.76
5
130
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.14
25.254
59
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.753
15
200
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.108
15
3
X-RAY DIFFRACTION
r_chiral_restr
0.065
0.2
143
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1234
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
209
X-RAY DIFFRACTION
r_nbd_refined
0.203
0.2
223
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.16
0.2
944
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.2
543
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.08
0.2
413
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.106
0.2
149
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.124
0.2
18
X-RAY DIFFRACTION
r_nbd_other
0.189
0.2
81
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.106
0.2
37
X-RAY DIFFRACTION
r_mcbond_it
0.949
2.045
511
X-RAY DIFFRACTION
r_mcbond_other
0.947
2.042
510
X-RAY DIFFRACTION
r_mcangle_it
1.618
4.59
638
X-RAY DIFFRACTION
r_mcangle_other
1.618
4.594
639
X-RAY DIFFRACTION
r_scbond_it
1.398
2.329
637
X-RAY DIFFRACTION
r_scbond_other
1.397
2.336
638
X-RAY DIFFRACTION
r_scangle_it
2.319
5.042
922
X-RAY DIFFRACTION
r_scangle_other
2.318
5.053
923
X-RAY DIFFRACTION
r_lrange_it
5.166
20.783
1426
X-RAY DIFFRACTION
r_lrange_other
5.164
20.812
1427
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.48-1.516
0.214
52
0.176
924
X-RAY DIFFRACTION
67.4499
1.516-1.557
0.253
61
0.177
1071
X-RAY DIFFRACTION
81.5562
1.557-1.602
0.202
61
0.173
1172
X-RAY DIFFRACTION
90.1975
1.602-1.652
0.204
82
0.177
1243
X-RAY DIFFRACTION
99.1025
1.652-1.706
0.24
66
0.17
1221
X-RAY DIFFRACTION
99.9224
1.706-1.766
0.2
70
0.176
1189
X-RAY DIFFRACTION
100
1.766-1.832
0.198
62
0.177
1133
X-RAY DIFFRACTION
99.9164
1.832-1.907
0.22
58
0.16
1113
X-RAY DIFFRACTION
99.8295
1.907-1.992
0.202
57
0.169
1075
X-RAY DIFFRACTION
99.9117
1.992-2.089
0.225
66
0.159
1000
X-RAY DIFFRACTION
100
2.089-2.201
0.174
57
0.144
962
X-RAY DIFFRACTION
99.609
2.201-2.335
0.167
57
0.148
915
X-RAY DIFFRACTION
99.5902
2.335-2.496
0.182
51
0.15
867
X-RAY DIFFRACTION
100
2.496-2.695
0.143
35
0.128
826
X-RAY DIFFRACTION
99.6528
2.695-2.952
0.169
35
0.148
754
X-RAY DIFFRACTION
99.8734
2.952-3.299
0.167
41
0.148
685
X-RAY DIFFRACTION
99.8624
3.299-3.808
0.164
15
0.128
628
X-RAY DIFFRACTION
99.8447
3.808-4.658
0.165
20
0.136
535
X-RAY DIFFRACTION
99.6409
4.658-6.566
0.192
22
0.159
425
X-RAY DIFFRACTION
99.7768
6.566-37
0.182
10
0.161
256
X-RAY DIFFRACTION
98.155
Refinement TLS params.
Method: refined / Origin x: -6.5656 Å / Origin y: 8.192 Å / Origin z: -16.9696 Å
11
12
13
21
22
23
31
32
33
T
0.0083 Å2
-0.0089 Å2
-0.0033 Å2
-
0.0269 Å2
0.0125 Å2
-
-
0.0116 Å2
L
0.6026 °2
-0.0637 °2
-0.3037 °2
-
0.0935 °2
-0.1152 °2
-
-
0.524 °2
S
-0.015 Å °
-0.0149 Å °
-0.0643 Å °
0.0278 Å °
-0.0278 Å °
-0.0086 Å °
-0.0357 Å °
0.0116 Å °
0.0427 Å °
Refinement TLS group
Selection: ALL
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