4QBM

Crystal structure of human BAZ2A bromodomain in complex with a diacetylated histone 4 peptide (H4K16acK20ac)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LZ2pdb entry 4LZ2, BAZ2A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.1M sodium phosphate monobasic, 0.1M potassium phosphate monobasic, 2 M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7655.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.869α = 90
b = 64.869β = 90
c = 71.637γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9763DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6529.010.0670.03615.68.5356333563318.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 4LZ2, BAZ2A1.6564.873563333458166198.220.186310.185340.20495RANDOM23.668
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]
0.240.24-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.843
r_dihedral_angle_4_deg17.702
r_dihedral_angle_3_deg11.079
r_long_range_B_refined5.377
r_long_range_B_other5.248
r_dihedral_angle_1_deg5.136
r_scangle_other3.629
r_scbond_it2.284
r_scbond_other2.282
r_mcangle_other2.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.843
r_dihedral_angle_4_deg17.702
r_dihedral_angle_3_deg11.079
r_long_range_B_refined5.377
r_long_range_B_other5.248
r_dihedral_angle_1_deg5.136
r_scangle_other3.629
r_scbond_it2.284
r_scbond_other2.282
r_mcangle_other2.134
r_mcangle_it2.132
r_angle_refined_deg1.386
r_mcbond_it1.359
r_mcbond_other1.353
r_angle_other_deg0.795
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1905
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms4

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling