3G0L | pdb_00003g0l

Crystal Structure of Human Bromodomain Adjacent to Zinc finger domain 2B (BAZ2B)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NXB	ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OO1	ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OSS	ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OUO	ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2RFJ	ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	3DAI	ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	0.1M MMT pH 6.0, 30% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.2	70.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.434	α = 90
b = 96.314	β = 90
c = 57.641	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		2008-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5

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	2.03	23.62	96.4	0.079	0.079	12.5	3.7	15105	14561			31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.14	94.4		0.606	0.606	2	3.7	2066

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	ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI	2.03	22.22	15201	14547	728	95.7	0.179	0.179	0.178	0.2	0.211	0.22	RANDOM	17.301

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]
2.01			-0.99		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.219
r_dihedral_angle_4_deg	17.664
r_dihedral_angle_3_deg	11.263
r_scangle_it	8.573
r_scbond_it	7.685
r_dihedral_angle_1_deg	5.159
r_mcangle_it	4.354
r_mcbond_it	3.128
r_angle_refined_deg	1.35
r_mcbond_other	1.051
r_angle_other_deg	0.899
r_chiral_restr	0.08
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	927
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction