9MR9 | pdb_00009mr9

Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HAY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.95	α = 90
b = 298.503	β = 90
c = 142.988	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER X 9M		2020-02-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12713	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	3.3	29.87	99	0.203	0.267	0.171	0.981	5.4	4.1		70695

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.37	99.7		1.19	1.554	0.989	0.503	1.1	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3.3	29.87	67156	3501	98.9	0.2216	0.2188	0.2187	0.2752	0.271	RANDOM	90.333

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]
-3.39		-0.91	1.98		1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.651
r_dihedral_angle_3_deg	18.411
r_dihedral_angle_4_deg	17.735
r_mcangle_it	8.531
r_dihedral_angle_1_deg	7.108
r_mcbond_it	5.082
r_mcbond_other	5.081
r_angle_refined_deg	1.596
r_angle_other_deg	1.178
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.651
r_dihedral_angle_3_deg	18.411
r_dihedral_angle_4_deg	17.735
r_mcangle_it	8.531
r_dihedral_angle_1_deg	7.108
r_mcbond_it	5.082
r_mcbond_other	5.081
r_angle_refined_deg	1.596
r_angle_other_deg	1.178
r_chiral_restr	0.089
r_bond_refined_d	0.011
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	30397
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	462

Software

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

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.