4XY8

Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HME

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.20M NaBr, 0.1M BTProp pH 7.5, 20.0% PEG 3350, 10.0% EtGly,

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.716	α = 90
b = 43.604	β = 104.34
c = 40.88	γ = 90

Symmetry
Space Group	C 1 2 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		2013-02-10	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)	Rrim I (All)	Rpim I (All)	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	1.7	19.559	97.7	0.086	0.086	0.09	0.029	20.3	9.6	14841	14841

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	95.2		0.337	0.337	0.115	7.4	9.4	2064

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3HME	1.7	19.54	14086	748	97.19	0.1502	0.1482	0.1857	RANDOM	15.873

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]
-0.23		-0.57	0.03		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.082
r_dihedral_angle_4_deg	15.703
r_dihedral_angle_3_deg	13.848
r_dihedral_angle_1_deg	4.559
r_mcangle_it	3.36
r_mcbond_other	2.558
r_mcbond_it	2.557
r_angle_refined_deg	1.747
r_angle_other_deg	0.828
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.082
r_dihedral_angle_4_deg	15.703
r_dihedral_angle_3_deg	13.848
r_dihedral_angle_1_deg	4.559
r_mcangle_it	3.36
r_mcbond_other	2.558
r_mcbond_it	2.557
r_angle_refined_deg	1.747
r_angle_other_deg	0.828
r_chiral_restr	0.093
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	920
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.