5DW1 | pdb_00005dw1

X-ray crystal structure of human BRD2(BD2) in complex with RVX297 to 1.55 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	2.6 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
3	59.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.289	α = 62.09
b = 57.318	β = 72.08
c = 62.033	γ = 66.08

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	CCD	ADSC QUANTUM 315r	Mirrors	2011-06-16	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	1.55	50	95	0.04	0.056	0.04	14.2	2		85026

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	1.61	93.6		0.426	0.602	0.426	0.645		2	8333

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	50	80774	4250	94.76	0.1607	0.1589	0.17	0.1948	0.2	RANDOM	28.174

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]
-0.59	0.23	0.13	0.28	-0.34	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.406
r_dihedral_angle_4_deg	20.981
r_dihedral_angle_3_deg	12.982
r_dihedral_angle_1_deg	5.063
r_mcangle_it	3.06
r_mcbond_it	2.226
r_mcbond_other	2.225
r_angle_refined_deg	2.213
r_angle_other_deg	1.112
r_chiral_restr	0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.406
r_dihedral_angle_4_deg	20.981
r_dihedral_angle_3_deg	12.982
r_dihedral_angle_1_deg	5.063
r_mcangle_it	3.06
r_mcbond_it	2.226
r_mcbond_other	2.225
r_angle_refined_deg	2.213
r_angle_other_deg	1.112
r_chiral_restr	0.131
r_bond_refined_d	0.025
r_gen_planes_refined	0.015
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3641
Nucleic Acid Atoms
Solvent Atoms	583
Heterogen Atoms	126

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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.