5FFW

Crystal structure of the bromodomain of human BRPF1 in complex with H4K5acK8ac histone peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277.150.2 M NaCl, 25% PEG3350, 0.1 M Hepes pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.3948.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.348α = 90
b = 93.177β = 90
c = 32.216γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-13MSINGLE 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
11.529.2699.40.0620.0221.510.8431144311413.698
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)
11.51.5896.20.6343.28.6

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 REPLACEMENTTHROUGHOUT4LC21.529.2640472213798.310.213780.212230.24307RANDOM23.558
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]
-0.52-1.431.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.615
r_dihedral_angle_4_deg19.567
r_dihedral_angle_3_deg11.748
r_long_range_B_refined5.179
r_dihedral_angle_1_deg5.022
r_long_range_B_other4.966
r_scangle_other2.678
r_mcangle_it1.92
r_mcangle_other1.919
r_scbond_it1.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.615
r_dihedral_angle_4_deg19.567
r_dihedral_angle_3_deg11.748
r_long_range_B_refined5.179
r_dihedral_angle_1_deg5.022
r_long_range_B_other4.966
r_scangle_other2.678
r_mcangle_it1.92
r_mcangle_other1.919
r_scbond_it1.65
r_scbond_other1.649
r_angle_refined_deg1.501
r_mcbond_it1.192
r_mcbond_other1.192
r_angle_other_deg0.795
r_chiral_restr0.082
r_bond_refined_d0.012
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 Atoms1913
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing