7WMU | pdb_00007wmu

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13146

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.41	α = 90
b = 35.57	β = 96.51
c = 73.563	γ = 90

Symmetry
Space Group	I 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	197	PIXEL	DECTRIS PILATUS 6M		2021-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

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	1.73	42.45	99.1	0.114	0.126	0.052	0.992	13.5	5.6		13041

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	1.73	1.76	98.1		0.819	0.905	0.377	0.772		5.6

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 (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	4QEW	1.73	42.45	12375	656	98.7	0.1518	0.1501	0.16	0.1847	0.19	RANDOM	16.534

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]
0.78		-0.29	-0.35		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.51
r_dihedral_angle_4_deg	23.67
r_dihedral_angle_3_deg	13.127
r_dihedral_angle_1_deg	4.694
r_angle_refined_deg	1.782
r_angle_other_deg	1.252
r_chiral_restr	0.092
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.51
r_dihedral_angle_4_deg	23.67
r_dihedral_angle_3_deg	13.127
r_dihedral_angle_1_deg	4.694
r_angle_refined_deg	1.782
r_angle_other_deg	1.252
r_chiral_restr	0.092
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	921
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	86

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	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.