4QC3 | pdb_00004qc3

Crystal structure of human BAZ2B bromodomain in complex with a diacetylated histone 4 peptide (H4K8acK12ac)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	18% PEG 8000, 0.2M calcium acetate, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.67	α = 90
b = 32.402	β = 109.82
c = 62.033	γ = 90

Symmetry
Space Group	P 1 21 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		2013-12-02	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	1.6	29.18	100	0.019	0.015	45.4	4.3	30743	30743			10.062

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	1.6	1.7	100		0.04	0.052	18.09	2.33	9355

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	Ensemble of PDB ENTRY 3G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY	1.6	29.179	29184	29184	1550	99.17	0.16866	0.16768	0.18	0.18697	0.19	RANDOM	14.502

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]
-0.32		0.03			0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.725
r_dihedral_angle_4_deg	20.022
r_dihedral_angle_3_deg	10.852
r_dihedral_angle_1_deg	4.537
r_long_range_B_refined	4.482
r_long_range_B_other	4.312
r_scangle_other	1.875
r_angle_refined_deg	1.307
r_scbond_it	1.213
r_scbond_other	1.212
r_mcangle_it	1.16
r_mcangle_other	1.16
r_angle_other_deg	0.758
r_mcbond_it	0.707
r_mcbond_other	0.705
r_chiral_restr	0.071
r_bond_refined_d	0.009
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	1787
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	12

Software

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