5DKC | pdb_00005dkc

Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3 chemical probe

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4QY4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277.15	19% PEG 6K, 4% ethyleneglycol, 0.01M ZnCl2

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.424	α = 90
b = 74.424	β = 90
c = 89.856	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.6	26.19	99.4	0.054	0.025	17.1	6.8	24515	24515

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.62	93.5		0.8	2.1	6

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	4QY4	1.6	26.19	23139	1375	99.47	0.19468	0.1937	0.2	0.21115	0.22	RANDOM	31.676

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]
0.31	0.15		0.31		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.094
r_dihedral_angle_3_deg	12.633
r_dihedral_angle_4_deg	11.114
r_long_range_B_refined	6.339
r_long_range_B_other	6.337
r_dihedral_angle_1_deg	5.433
r_scangle_other	5.025
r_scbond_other	3.125
r_scbond_it	3.123
r_mcangle_it	2.88
r_mcangle_other	2.877
r_mcbond_it	1.977
r_mcbond_other	1.977
r_angle_refined_deg	1.521
r_angle_other_deg	0.968
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	908
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	25

Software

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