5IG6

Ultra-high resolution crystal structure of second bromodomain of BRD2 in complex with inhibitor 6B3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E3K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.530030% PEG MME 2000, 50mM Tris-HCl pH 7.5, 50mM NaCl, 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.2244.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32α = 90
b = 52.37β = 90
c = 71.46γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.7293ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
10.9142.2299.40.0540.0540.99911.64.4860547.031
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)
10.910.961001.6270.94.1

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 REPLACEMENTTHROUGHOUT2E3k0.912081790432899.160.12620.125260.14336RANDOM12.231
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]
0.170.06-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.68
r_sphericity_free26.73
r_dihedral_angle_4_deg21.56
r_dihedral_angle_3_deg12.673
r_sphericity_bonded7.999
r_dihedral_angle_1_deg4.866
r_rigid_bond_restr3.674
r_angle_refined_deg1.812
r_angle_other_deg0.947
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.68
r_sphericity_free26.73
r_dihedral_angle_4_deg21.56
r_dihedral_angle_3_deg12.673
r_sphericity_bonded7.999
r_dihedral_angle_1_deg4.866
r_rigid_bond_restr3.674
r_angle_refined_deg1.812
r_angle_other_deg0.947
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_gen_planes_other0.007
r_bond_other_d0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms945
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction