3Q2E

Crystal structure of the second bromodomain of human bromodomain and WD repeat-containing protein 1 isoform A (WDR9)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.2M (NH4)COOCH3, 0.1M BisTris, 25% PEG 3350 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.66	α = 90
b = 51.66	β = 90
c = 151.36	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2010-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9700	Diamond	I02

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	1.74	28.892	99.5	0.088	0.088	12.9	6.7	13033	12968			25.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.74	1.83	98		0.87	0.87	0.951	0.375	0.9	6.1	1797

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	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY	1.74	28.89	13042	12942	634	99.23	0.1867	0.1867	0.1852	0.2191	RANDOM	29.4449

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]
0.2	0.1		0.2		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.635
r_dihedral_angle_3_deg	13.363
r_dihedral_angle_4_deg	12.969
r_scangle_it	10.535
r_scbond_it	7.593
r_dihedral_angle_1_deg	4.915
r_mcangle_it	4.675
r_mcbond_it	2.988
r_angle_refined_deg	1.45
r_angle_other_deg	0.934

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.635
r_dihedral_angle_3_deg	13.363
r_dihedral_angle_4_deg	12.969
r_scangle_it	10.535
r_scbond_it	7.593
r_dihedral_angle_1_deg	4.915
r_mcangle_it	4.675
r_mcbond_it	2.988
r_angle_refined_deg	1.45
r_angle_other_deg	0.934
r_mcbond_other	0.909
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	862
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	4

Software

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