3Q2F | pdb_00003q2f

Crystal Structure of the bromodomain of human BAZ2B in complex with a triazolo ligand

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	7.5	277	24% PEG 1K 20% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.17	70.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.31	α = 90
b = 96.35	β = 90
c = 57.25	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		2010-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.06	62.583	100	0.171	6.4	6.8	14455	14455

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.06	2.17	100		0.748	0.748	0.813	0.314	1	6.6	2082

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.06	31.29	14447	14401	725	99.68	0.1964	0.1964	0.1941	0.19	0.242	0.23	RANDOM	31.6747

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]
1.54			-0.1		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.245
r_dihedral_angle_4_deg	22.784
r_dihedral_angle_3_deg	14.535
r_scangle_it	8.457
r_scbond_it	7.258
r_dihedral_angle_1_deg	5.811
r_mcangle_it	4.755
r_mcbond_it	3.374
r_angle_refined_deg	1.596
r_mcbond_other	1.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.245
r_dihedral_angle_4_deg	22.784
r_dihedral_angle_3_deg	14.535
r_scangle_it	8.457
r_scbond_it	7.258
r_dihedral_angle_1_deg	5.811
r_mcangle_it	4.755
r_mcbond_it	3.374
r_angle_refined_deg	1.596
r_mcbond_other	1.092
r_angle_other_deg	0.92
r_chiral_restr	0.079
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	923
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	33

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
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 R01GM157729.