4NRA

Crystal Structure of the bromodomain of human BAZ2B in complex with compound-6 E11322


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G0Lpdb entry 3G0L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277.1528% low MW PEG Smears, 0.1M MES pH 6.5, 15%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
4.1670.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.477α = 90
b = 96.377β = 90
c = 57.705γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8519.5299.80.07811.45197281970629.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.951000.6582.152816

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 3G0L1.8519.5221970618697100799.650.178960.177250.21227RANDOM38.842
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]
2.47-0.9-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.187
r_dihedral_angle_4_deg23.244
r_dihedral_angle_3_deg12.812
r_long_range_B_refined10.094
r_long_range_B_other10.093
r_scangle_other7.423
r_dihedral_angle_1_deg6.033
r_scbond_it5.921
r_scbond_other5.919
r_mcangle_other4.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.187
r_dihedral_angle_4_deg23.244
r_dihedral_angle_3_deg12.812
r_long_range_B_refined10.094
r_long_range_B_other10.093
r_scangle_other7.423
r_dihedral_angle_1_deg6.033
r_scbond_it5.921
r_scbond_other5.919
r_mcangle_other4.885
r_mcangle_it4.85
r_mcbond_it4.013
r_mcbond_other3.99
r_angle_refined_deg1.567
r_angle_other_deg0.937
r_chiral_restr0.09
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms937
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms37

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling