7WNI | pdb_00007wni

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13158

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6E6J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M Sodium malonate pH 4.0, 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.685	α = 90
b = 108.685	β = 90
c = 81.58	γ = 90

Symmetry
Space Group	P 41 21 2

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 PILATUS3 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	3.12	76.85	99.9	0.301	0.332	0.136	0.798	4	5.5		9140

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	3.12	3.34	100		0.739	0.813	0.331	0.819		5.5

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	6E6J	3.12	76.85	8654	461	99.75	0.2104	0.2078	0.21	0.2575	0.25	RANDOM	46.485

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]
-5.34			-5.34		10.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.515
r_dihedral_angle_4_deg	23.79
r_dihedral_angle_3_deg	19.181
r_dihedral_angle_1_deg	6.227
r_angle_refined_deg	1.711
r_angle_other_deg	0.989
r_chiral_restr	0.073
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.515
r_dihedral_angle_4_deg	23.79
r_dihedral_angle_3_deg	19.181
r_dihedral_angle_1_deg	6.227
r_angle_refined_deg	1.711
r_angle_other_deg	0.989
r_chiral_restr	0.073
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1802
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	107

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.