5HFR

Crystal structure of the second bromodomain H395R mutant of human BRD3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M sodium nitrate, 10 % PEG 3350, 5 % EDO, 0.1 M bis tris prop. pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.9758.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.828α = 90
b = 92.546β = 90
c = 102.954γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-06MSINGLE 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
11.729.5599.30.2340.071312.76893568935
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)
11.71.7387.42.4832.710.3

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 REPLACEMENTTHROUGHOUT2OO11.729.5565516334899.260.1950.193690.22086RANDOM20.09
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]
-1.01-0.41.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.808
r_dihedral_angle_4_deg19.98
r_dihedral_angle_3_deg11.724
r_long_range_B_refined5.109
r_long_range_B_other5.109
r_dihedral_angle_1_deg5.082
r_scangle_other3.149
r_scbond_it1.987
r_scbond_other1.984
r_mcangle_other1.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.808
r_dihedral_angle_4_deg19.98
r_dihedral_angle_3_deg11.724
r_long_range_B_refined5.109
r_long_range_B_other5.109
r_dihedral_angle_1_deg5.082
r_scangle_other3.149
r_scbond_it1.987
r_scbond_other1.984
r_mcangle_other1.736
r_mcangle_it1.735
r_angle_refined_deg1.486
r_mcbond_it1.111
r_mcbond_other1.108
r_angle_other_deg0.86
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3628
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing