5MGM

Crystal Structure of BAZ2A bromodomain in complex with acetophenone derivative 4

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	20% PEG3350, 0.2 M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.861	α = 90
b = 94.861	β = 90
c = 32.75	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	DECTRIS PILATUS 2M		2016-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.00	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	27.38	99.5	0.318	0.984	7.1	9.8		4298

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	100		1.347	0.699		8.7

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	FREE R-VALUE	4LZ2	2.8	27.38	4109	187	99.1	0.2195	0.2181	0.2518	RANDOM	41.931

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]
13.16			13.16		-26.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.239
r_dihedral_angle_4_deg	13.716
r_dihedral_angle_3_deg	10.968
r_dihedral_angle_1_deg	4
r_mcangle_it	2.094
r_mcbond_it	1.147
r_mcbond_other	1.13
r_angle_refined_deg	0.873
r_angle_other_deg	0.676
r_chiral_restr	0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.239
r_dihedral_angle_4_deg	13.716
r_dihedral_angle_3_deg	10.968
r_dihedral_angle_1_deg	4
r_mcangle_it	2.094
r_mcbond_it	1.147
r_mcbond_other	1.13
r_angle_refined_deg	0.873
r_angle_other_deg	0.676
r_chiral_restr	0.047
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	829
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	16

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
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 R01GM133198.