4QC1 | pdb_00004qc1

Crystal structure of human BAZ2B bromodomain in complex with an acetylated histone 3 peptide (H3K14ac)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DVV	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY
experimental model	PDB	1X0J	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY
experimental model	PDB	3DAI	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY
experimental model	PDB	3HMH	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY
experimental model	PDB	2GRC	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY
experimental model	PDB	2OO1	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY
experimental model	PDB	2OSS	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY
experimental model	PDB	3D7C	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY
experimental model	PDB	3DWY	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	277	0.1M MES, 0.01M zinc sulfatE, 25% PEG methyl ether 550, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.724	α = 90
b = 67.012	β = 90
c = 136.055	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 6M		2013-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9796	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	1.99	29.039	100	0.068	0.035	17.6	8.4	19403	19403			22.83

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	1.99	2.11	100		0.51	0.578	3.08	4.4	5642

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 (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	Ensamble of pdb id G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY	1.99	29.039	18364	18364	987	99.6	0.21451	0.21225	0.22	0.25575	0.26	RANDOM	37.188

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]
-0.47			3.42		-2.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.017
r_dihedral_angle_4_deg	18.014
r_dihedral_angle_3_deg	15.572
r_long_range_B_refined	6.563
r_long_range_B_other	6.524
r_dihedral_angle_1_deg	6.348
r_scangle_other	4.511
r_mcangle_it	3.865
r_mcangle_other	3.863
r_scbond_it	3.103
r_scbond_other	3.023
r_mcbond_it	2.577
r_mcbond_other	2.575
r_angle_refined_deg	1.658
r_angle_other_deg	0.861
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1860
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	9

Software

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