3Q2E | pdb_00003q2e

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MB3	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OSS	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OUO	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2GRC	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	2OO1	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3DAI	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3D7C	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY
experimental model	PDB	3DWY	3MB3, 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.19	0.2191	0.22	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
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