4IR4 | pdb_00004ir4

Crystal Structure of the bromodomain of human BAZ2B in complex with 1-[7-(morpholin-4-yl)-1-(pyridin-2-yl)indolizin-3-yl]ethanone (GSK2834113A)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3G0L	PDB entry 3G0L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.25	277.15	32% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.25 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution), VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.699	α = 90
b = 96.465	β = 90
c = 57.741	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	100	IMAGE PLATE	RIGAKU RAXIS IV		2011-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.05	19.68	99.8	0.12	7.9	5	14789	14774			30.8

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	2.05	2.16	99.8		0.791	2	5.1	2097

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	PDB entry 3G0L	2.05	19.6	2	14774	14026	747	99.56	0.18582	0.18376	0.2	0.2276	0.24	RANDOM	44.822

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]
4.37			-1.68		-2.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.876
r_dihedral_angle_4_deg	14.07
r_dihedral_angle_3_deg	12.742
r_dihedral_angle_1_deg	5.764
r_angle_refined_deg	1.577
r_angle_other_deg	0.882
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.876
r_dihedral_angle_4_deg	14.07
r_dihedral_angle_3_deg	12.742
r_dihedral_angle_1_deg	5.764
r_angle_refined_deg	1.577
r_angle_other_deg	0.882
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	937
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	56

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

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.