5CRZ | pdb_00005crz

Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MXF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.92	α = 90
b = 47.34	β = 90
c = 78.37	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	PSI PILATUS 6M		2015-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	OTHER	0.97852

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.12	78.37	94.1	0.097	0.039	0.993	10.8	7.4		7346

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.18	99.7		0.251	0.094	0.985	5.7	8.1	640

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	3MXF	2.12	40.52	6935	375	93.6	0.2274	0.2258	0.23	0.2567	0.25	RANDOM	32.145

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]
6.55			-2.82		-3.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.983
r_dihedral_angle_3_deg	12.855
r_dihedral_angle_4_deg	10.809
r_dihedral_angle_1_deg	5.243
r_mcangle_it	1.306
r_angle_refined_deg	1.108
r_angle_other_deg	0.883
r_mcbond_other	0.726
r_mcbond_it	0.725
r_chiral_restr	0.054

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.983
r_dihedral_angle_3_deg	12.855
r_dihedral_angle_4_deg	10.809
r_dihedral_angle_1_deg	5.243
r_mcangle_it	1.306
r_angle_refined_deg	1.108
r_angle_other_deg	0.883
r_mcbond_other	0.726
r_mcbond_it	0.725
r_chiral_restr	0.054
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1115
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	45

Software

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