5HEM

Crystal structure of the N-terminus D161Y bromodomain mutant of human BRD2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527715% PEG3350, 0.1M bis-tris propane pH 6.6, 10% ethylene glycol, 0.15M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.2545.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.73α = 90
b = 68.73β = 90
c = 113.364γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-04-25MSINGLE 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
11.6529.6799.70.1080.0513.863356433564
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)
11.651.6895.50.334.13.6

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 REPLACEMENTTHROUGHOUT4ALH1.6529.6731894160999.650.168230.166680.19888RANDOM16.245
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]
0.210.21-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.324
r_dihedral_angle_4_deg26.882
r_dihedral_angle_3_deg11.767
r_dihedral_angle_1_deg5.19
r_long_range_B_refined4.643
r_long_range_B_other4.393
r_scangle_other2.59
r_angle_refined_deg1.663
r_scbond_it1.625
r_scbond_other1.624
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.324
r_dihedral_angle_4_deg26.882
r_dihedral_angle_3_deg11.767
r_dihedral_angle_1_deg5.19
r_long_range_B_refined4.643
r_long_range_B_other4.393
r_scangle_other2.59
r_angle_refined_deg1.663
r_scbond_it1.625
r_scbond_other1.624
r_mcangle_it1.486
r_mcangle_other1.486
r_angle_other_deg0.95
r_mcbond_it0.905
r_mcbond_other0.892
r_chiral_restr0.106
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.002
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 Atoms1982
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing