6WVX | pdb_00006wvx

Crystal structure of the first bromodomain of human BRD4 with benzodiazepine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Z1S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.18 M Triammonium Citrate, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.43	α = 82.21
b = 39.71	β = 75.25
c = 57.82	γ = 89.86

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 2M		2016-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.55	55.368	88.7	0.089	0.126	0.089	0.987	3.2	1.5		33390

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	90.2		0.531	0.751	0.531	0.601

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4Z1S	1.55	39.32	33176	1681	88.119	0.218	0.2168	0.23	0.2462	0.26	12.361

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.658	0.002	0.489	0.283	0.302	0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.355
r_dihedral_angle_3_deg	14.553
r_dihedral_angle_4_deg	12.613
r_dihedral_angle_1_deg	5.786
r_lrange_it	3.597
r_lrange_other	3.517
r_scangle_it	2.338
r_scangle_other	2.337
r_mcangle_it	1.677
r_mcangle_other	1.677
r_angle_refined_deg	1.594
r_scbond_it	1.503
r_scbond_other	1.502
r_angle_other_deg	1.431
r_mcbond_it	1.012
r_mcbond_other	1.012
r_nbd_refined	0.217
r_nbd_other	0.214
r_symmetry_nbd_refined	0.201
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.16
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2090
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing