4NR7

Crystal structure of the bromodomain of human CREBBP in complex with an isoxazolyl-benzimidazole ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DWYPDB entry 3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62770.20M NH4Cl, 0.1M MES pH 6.0, 20.0% PEG 6K, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4950.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.344α = 90
b = 49.827β = 90
c = 80.554γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

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
11.249.8397.90.0320.03227.66.5452774432610.7
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)RedundancyNumber Unique Reflections (All)
11.21.2695.30.3080.3082.66.56199

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 3DWY1.242.3842313195497.70.127790.127060.14371RANDOM15.518
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]
0.110.21-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.761
r_sphericity_free24.912
r_dihedral_angle_4_deg13.325
r_dihedral_angle_3_deg11.702
r_sphericity_bonded8.991
r_dihedral_angle_1_deg5.148
r_long_range_B_refined3.509
r_rigid_bond_restr3.211
r_scangle_other3.096
r_long_range_B_other2.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.761
r_sphericity_free24.912
r_dihedral_angle_4_deg13.325
r_dihedral_angle_3_deg11.702
r_sphericity_bonded8.991
r_dihedral_angle_1_deg5.148
r_long_range_B_refined3.509
r_rigid_bond_restr3.211
r_scangle_other3.096
r_long_range_B_other2.814
r_scbond_it2.722
r_scbond_other2.721
r_mcangle_other1.805
r_mcangle_it1.797
r_mcbond_other1.485
r_angle_refined_deg1.483
r_mcbond_it1.482
r_angle_other_deg0.801
r_chiral_restr0.093
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms971
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms48

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction