5I89

Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepinone G02857790


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.150.2 M calcium acetate hydrate, and 20% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2645.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.283α = 90
b = 34.321β = 106.82
c = 40.005γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9786APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.0750990.0690.0830.04511.63.553632
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)
11.071.1197.30.2073.4

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 3DWY1.0745.1350979265398.940.11760.11650.1371RANDOM13.397
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]
-0.09-0.090.26-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.246
r_sphericity_free34.5
r_sphericity_bonded14.702
r_dihedral_angle_3_deg11.977
r_dihedral_angle_4_deg10.181
r_rigid_bond_restr6.971
r_dihedral_angle_1_deg6.335
r_mcangle_it4.983
r_mcbond_it3.939
r_mcbond_other3.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.246
r_sphericity_free34.5
r_sphericity_bonded14.702
r_dihedral_angle_3_deg11.977
r_dihedral_angle_4_deg10.181
r_rigid_bond_restr6.971
r_dihedral_angle_1_deg6.335
r_mcangle_it4.983
r_mcbond_it3.939
r_mcbond_other3.935
r_angle_refined_deg1.38
r_angle_other_deg0.726
r_chiral_restr0.076
r_gen_planes_refined0.018
r_bond_refined_d0.009
r_gen_planes_other0.005
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms967
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms31

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing