4IOQ | pdb_00004ioq

Crystal Structure of the first bromodomain of BRD4 in complex with pyrrolidin-2-one

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	277	16% PEG 3350, 20% ethylene glycol , pH 7.5, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.309	α = 90
b = 44.396	β = 90
c = 78.157	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	PIXEL	DECTRIS PILATUS 2M		2011-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.200	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.5	39.08	99.3	0.076	7.9	2.9	21286	21286

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.58	98.8		0.373	0.373	1.9	2.7	3007

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.5	39.08	21469	21222	1080	98.85	0.171	0.1707	0.1695	0.17	0.194	0.19	RANDOM	13.6828

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]
10.33			-0.31		-10.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.55
r_dihedral_angle_3_deg	12.902
r_sphericity_free	12.426
r_dihedral_angle_4_deg	10.054
r_rigid_bond_restr	6.909
r_dihedral_angle_1_deg	5.278
r_sphericity_bonded	5.202
r_angle_refined_deg	1.456
r_chiral_restr	0.092
r_bond_refined_d	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.55
r_dihedral_angle_3_deg	12.902
r_sphericity_free	12.426
r_dihedral_angle_4_deg	10.054
r_rigid_bond_restr	6.909
r_dihedral_angle_1_deg	5.278
r_sphericity_bonded	5.202
r_angle_refined_deg	1.456
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1052
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

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.