5DW2

X-ray crystal structure of human BRD4(BD1) in complex with RVX297 to 1.12 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	298	30% PEG2000 MME, 0.1 M potassium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.279	α = 90
b = 44.656	β = 90
c = 78.015	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r	Mirrors	2011-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.075	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.12	50	99.4	0.055	0.061	0.026	8.3	5.4		50572

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	1.12	1.16	98.6		0.458	0.508	0.216	0.885		5.3	4921

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.12	39.01	47942	2566	99.32	0.1243	0.1229	0.1513	RANDOM	12.472

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]
0.1			-0.5		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.581
r_sphericity_free	32.585
r_dihedral_angle_3_deg	13.573
r_sphericity_bonded	10.645
r_dihedral_angle_4_deg	8.745
r_rigid_bond_restr	6.538
r_dihedral_angle_1_deg	5.423
r_angle_refined_deg	2.679
r_mcangle_it	1.717
r_mcbond_it	1.462

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.581
r_sphericity_free	32.585
r_dihedral_angle_3_deg	13.573
r_sphericity_bonded	10.645
r_dihedral_angle_4_deg	8.745
r_rigid_bond_restr	6.538
r_dihedral_angle_1_deg	5.423
r_angle_refined_deg	2.679
r_mcangle_it	1.717
r_mcbond_it	1.462
r_mcbond_other	1.461
r_angle_other_deg	1.374
r_chiral_restr	0.149
r_bond_refined_d	0.032
r_gen_planes_refined	0.017
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1062
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	64

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.