5BT5

Crystal structure of BRD2 second bromodomain in complex with SGC-CBP30 chemical probe


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M sodium/potassium tartrate, 20% PEG 3350, 10% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.2745.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.761α = 90
b = 71.806β = 90
c = 31.996γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.442.5299.30.0790.02722.39.2224988245075.314
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)
11.41.4895.90.16511.67.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.442.5223265120399.180.160780.15970.18204RANDOM11.732
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]
0.01-0.240.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.945
r_dihedral_angle_4_deg23.617
r_dihedral_angle_3_deg11.239
r_long_range_B_refined5.048
r_dihedral_angle_1_deg4.867
r_long_range_B_other4.722
r_scangle_other2.256
r_angle_refined_deg1.565
r_scbond_it1.372
r_scbond_other1.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.945
r_dihedral_angle_4_deg23.617
r_dihedral_angle_3_deg11.239
r_long_range_B_refined5.048
r_dihedral_angle_1_deg4.867
r_long_range_B_other4.722
r_scangle_other2.256
r_angle_refined_deg1.565
r_scbond_it1.372
r_scbond_other1.371
r_mcangle_other1.347
r_mcangle_it1.343
r_angle_other_deg1.289
r_mcbond_it0.792
r_mcbond_other0.757
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms910
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing