5FH7

Crystal structure of the fifth bromodomain of human PB1 in complex with compound 18


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q0O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277.150.1 M magnesium formate, 15% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9558.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.98α = 90
b = 59.21β = 90
c = 138.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-07-12MSINGLE 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
11.4759.2195.20.0520.0221.47.85693456934
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)
11.476.5768.30.5652.12.8

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 REPLACEMENTTHROUGHOUT4Q0O1.4754.5354004285794.930.187850.186810.2085RANDOM24.183
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]
0.070.59-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.908
r_dihedral_angle_4_deg15.505
r_dihedral_angle_3_deg12.296
r_long_range_B_refined6.017
r_long_range_B_other5.813
r_dihedral_angle_1_deg4.668
r_scangle_other3.667
r_scbond_it2.274
r_scbond_other2.273
r_mcangle_it1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.908
r_dihedral_angle_4_deg15.505
r_dihedral_angle_3_deg12.296
r_long_range_B_refined6.017
r_long_range_B_other5.813
r_dihedral_angle_1_deg4.668
r_scangle_other3.667
r_scbond_it2.274
r_scbond_other2.273
r_mcangle_it1.93
r_mcangle_other1.929
r_angle_refined_deg1.649
r_mcbond_it1.242
r_mcbond_other1.241
r_angle_other_deg0.979
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms1912
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing