4NQN | pdb_00004nqn

Crystal Structure of the bromodomain of human BRD9 in complex with a triazolo-phthalazine ligand

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	20% PEG 3350, 0.20M KSCN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.12	α = 90
b = 48.42	β = 90
c = 69.32	γ = 90

Symmetry
Space Group	P 21 21 21

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		2011-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	1.73	24.21	99.9	0.06	0.06	12.6	4.4	17164	17147			27.5

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	1.73	1.82	99.9		0.523	0.523	2	4.1	2345

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	PDB ENTRY 3HME	1.73	24.21	17114	17099	866	99.91	0.1904	0.1904	0.1877	0.19	0.2448	0.24	RANDOM	31.3741

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]
0.81			1.5		-2.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.285
r_dihedral_angle_3_deg	13.538
r_dihedral_angle_4_deg	13.442
r_dihedral_angle_1_deg	4.224
r_angle_refined_deg	1.587
r_angle_other_deg	0.872
r_chiral_restr	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.285
r_dihedral_angle_3_deg	13.538
r_dihedral_angle_4_deg	13.442
r_dihedral_angle_1_deg	4.224
r_angle_refined_deg	1.587
r_angle_other_deg	0.872
r_chiral_restr	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	911
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	37

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 R01GM157729.