4LZ2 | pdb_00004lz2

Crystal structure of the bromodomain of human BAZ2A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GOL	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	1DVV	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	1X0J	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	3DAI	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	3HMH	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	2GRC	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	2OO1	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	2OSS	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	3D7C	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY
experimental model	PDB	3DWY	PDB ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.4	277	22% PEG3350, 0.1 M Tris, pH 8.4, 0.25 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.417	α = 90
b = 95.417	β = 90
c = 33.054	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 6M		2013-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9686	Diamond	I04

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	1.76	27.56	100	0.063	0.021	20	9.9	17392	17392			30.4

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	1.76	1.86	100		0.85	0.85	2.6	9.7	2512

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 ENTRIES 3GOL, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, AND 3DWY	1.76	27.56	16501	16501	880	99.96	0.178	0.178	0.17598	0.19	0.21719	0.22	RANDOM	39.299

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]
0.54	0.54		0.54		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.646
r_dihedral_angle_4_deg	19.661
r_dihedral_angle_3_deg	13.736
r_long_range_B_other	11.192
r_long_range_B_refined	11.147
r_scangle_other	10.348
r_scbond_other	9.763
r_scbond_it	9.745
r_mcangle_it	6.693
r_mcangle_other	6.69
r_mcbond_it	5.779
r_mcbond_other	5.727
r_dihedral_angle_1_deg	5.359
r_angle_refined_deg	1.624
r_angle_other_deg	0.893
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	829
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	17

Software

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