9DU0 | pdb_00009du0

Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a SMARCA-BD binder

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.025~0.1 M zinc acetate, 16~26% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.558	α = 90
b = 64.558	β = 90
c = 89.083	γ = 120

Symmetry
Space Group	P 31

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 EIGER X 16M		2020-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979183	SSRF	BL17U1

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	47.4	98.4	0.132	0.17	0.105	0.992	5.3	2.3		8198

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	3.18			0.827	1.073	0.674	0.674

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	3	47.4	6909	364	87.47	0.2285	0.2231	0.2302	0.3381	0.3347	RANDOM	83.308

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]
2.98	1.49		2.98		-9.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.387
r_dihedral_angle_3_deg	22.988
r_dihedral_angle_4_deg	18.651
r_mcangle_it	8.863
r_dihedral_angle_1_deg	7.142
r_mcbond_it	5.479
r_mcbond_other	5.478
r_angle_refined_deg	1.406
r_angle_other_deg	1.084
r_chiral_restr	0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.387
r_dihedral_angle_3_deg	22.988
r_dihedral_angle_4_deg	18.651
r_mcangle_it	8.863
r_dihedral_angle_1_deg	7.142
r_mcbond_it	5.479
r_mcbond_other	5.478
r_angle_refined_deg	1.406
r_angle_other_deg	1.084
r_chiral_restr	0.046
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2832
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	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.