7WMQ

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13157


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6E6J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2773.5 M Sodium formate, 0.1 M Sodium acetate trihydrate pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.766.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.08α = 90
b = 95.08β = 90
c = 110.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray197PIXELDECTRIS PILATUS3 6M2021-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97915SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.3772.0495.90.1890.2070.0830.9867.26.137617
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.372.461000.8650.9510.3910.7135.8

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 REPLACEMENTTHROUGHOUT6E6J2.3772.0435719182795.820.18850.18740.2109RANDOM29.293
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]
1.78-0.81-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.769
r_dihedral_angle_4_deg18.249
r_dihedral_angle_3_deg15.523
r_dihedral_angle_1_deg4.806
r_angle_refined_deg1.409
r_angle_other_deg1.056
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.769
r_dihedral_angle_4_deg18.249
r_dihedral_angle_3_deg15.523
r_dihedral_angle_1_deg4.806
r_angle_refined_deg1.409
r_angle_other_deg1.056
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3649
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms241

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing