5I83

Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepinone G02773986


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 potassium thiocyanate, 0.1 M Bis-Tris, pH 5.5, 5% v/v ethylene glycol, 23% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5451.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.832α = 90
b = 50.885β = 90
c = 80.534γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002012-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

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
11.355099.80.0810.25.730903
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)
11.351.41000.6315.8

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 3DWY1.3531.5829268155199.410.14670.14440.1877RANDOM20.686
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]
-0.492.37-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.639
r_sphericity_free27.356
r_dihedral_angle_4_deg13.534
r_sphericity_bonded12.354
r_dihedral_angle_3_deg12.35
r_rigid_bond_restr6.094
r_dihedral_angle_1_deg5.769
r_mcangle_it2.746
r_mcbond_it2.33
r_mcbond_other2.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.639
r_sphericity_free27.356
r_dihedral_angle_4_deg13.534
r_sphericity_bonded12.354
r_dihedral_angle_3_deg12.35
r_rigid_bond_restr6.094
r_dihedral_angle_1_deg5.769
r_mcangle_it2.746
r_mcbond_it2.33
r_mcbond_other2.24
r_angle_refined_deg1.463
r_angle_other_deg0.758
r_chiral_restr0.093
r_gen_planes_refined0.014
r_bond_refined_d0.01
r_gen_planes_other0.002
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms962
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms25

Software

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