5T4U

Crystal structure of the bromodomain of human BRPF1 in complex with a quinolinone ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LC2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277.1520 % PEG3350, 0.2 M ammonium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.4349.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.315α = 90
b = 60.315β = 90
c = 63.389γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9686DiamondI04

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
11.527.231000.0720.0240.99817.89.52183820681118.293
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.531000.350.9394.97.7

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 REPLACEMENTTHROUGHOUT4LC21.527.2320751106199.980.207550.206340.23079RANDOM23.609
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]
-0.25-0.13-0.250.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.567
r_dihedral_angle_4_deg17.165
r_dihedral_angle_3_deg11.157
r_long_range_B_refined5.531
r_long_range_B_other5.423
r_dihedral_angle_1_deg4.691
r_scangle_other4.218
r_scbond_it2.738
r_scbond_other2.735
r_mcangle_other2.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.567
r_dihedral_angle_4_deg17.165
r_dihedral_angle_3_deg11.157
r_long_range_B_refined5.531
r_long_range_B_other5.423
r_dihedral_angle_1_deg4.691
r_scangle_other4.218
r_scbond_it2.738
r_scbond_other2.735
r_mcangle_other2.3
r_mcangle_it2.297
r_angle_refined_deg1.656
r_mcbond_it1.654
r_mcbond_other1.596
r_angle_other_deg0.856
r_chiral_restr0.099
r_bond_refined_d0.015
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 Atoms934
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing