5MQ1 | pdb_00005mq1

Crystal structure of the BRD7 bromodomain in complex with BI-9564

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		BRD9 in complex with TB-472

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	20% PEG6000, 10%EDO, 0.1 M HEPES pH 7.0, 0.01 M ZnCl2

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.87	α = 90
b = 125.255	β = 90
c = 37.353	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 6M		2016-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.5	35.42	99.7	10.4	6.6		25529

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		2.1	6.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	BRD9 in complex with TB-472	1.5	35.42	24238	1286	99.59	0.16337	0.16191	0.17	0.19033	0.19	RANDOM	13.488

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]
0.39			-0.6		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.557
r_dihedral_angle_3_deg	15.037
r_long_range_B_refined	6.063
r_long_range_B_other	5.514
r_dihedral_angle_4_deg	5.229
r_dihedral_angle_1_deg	4.973
r_scangle_other	2.299
r_angle_refined_deg	1.942
r_mcangle_it	1.822
r_mcangle_other	1.821
r_scbond_it	1.575
r_scbond_other	1.545
r_angle_other_deg	1.116
r_mcbond_it	1.058
r_mcbond_other	1.054
r_chiral_restr	0.118
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	880
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing