3UVD

Crystal Structure of the bromodomain of human Transcription activator BRG1 (SMARCA4) in complex with N-Methyl-2-pyrrolidone

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GRC	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	2OSS	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	2OUO	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	2OO1	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	3DAI	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	3D7C	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	3DWY	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	3G0L	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	3G0J	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3
experimental model	PDB	3GG3	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	28% MMW PEG smear 0.1M Tris.HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.2	α = 90
b = 29.89	β = 90.45
c = 67.06	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2010-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.52

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	29.89	100	0.067	0.067	10	3.5	10488	10488			35.1

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	1.85	1.95	100		0.544	0.544	1.4	3.4	1502

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3	1.85	29.89	10482	10479	502	99.97	0.2027	0.2027	0.1996	0.2624	RANDOM	46.1641

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]
-1.67		-0.82	2.13		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.184
r_dihedral_angle_4_deg	18.259
r_dihedral_angle_3_deg	17.639
r_dihedral_angle_1_deg	5.846
r_angle_refined_deg	1.722
r_angle_other_deg	1.035
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.184
r_dihedral_angle_4_deg	18.259
r_dihedral_angle_3_deg	17.639
r_dihedral_angle_1_deg	5.846
r_angle_refined_deg	1.722
r_angle_other_deg	1.035
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	990
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	7

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

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 R01GM133198.