5HRX

Crystal structure of the fifth bromodomain of human PB1 in complex with 1-butylisochromeno[3,4-c]pyrazol-5(2H)-one) compound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G0J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1M lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 30% PEG4K
Crystal Properties
Matthews coefficientSolvent content
2.1843.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.181α = 90
b = 58.42β = 90
c = 105.841γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9207DiamondI04-1

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
11.7329.2197.80.0510.02617.35.62682326823
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)
11.731.7696.30.8931.85

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 REPLACEMENTTHROUGHOUT3G0J1.7329.2125441133597.350.21580.213810.25373RANDOM32.679
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]
0.440.46-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.724
r_dihedral_angle_4_deg17.608
r_dihedral_angle_3_deg15.196
r_dihedral_angle_1_deg5.421
r_long_range_B_refined5.341
r_long_range_B_other5.34
r_scangle_other3.548
r_scbond_it2.246
r_scbond_other2.245
r_mcangle_it2.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.724
r_dihedral_angle_4_deg17.608
r_dihedral_angle_3_deg15.196
r_dihedral_angle_1_deg5.421
r_long_range_B_refined5.341
r_long_range_B_other5.34
r_scangle_other3.548
r_scbond_it2.246
r_scbond_other2.245
r_mcangle_it2.078
r_mcangle_other2.077
r_angle_refined_deg1.888
r_mcbond_it1.357
r_mcbond_other1.357
r_angle_other_deg1.218
r_chiral_restr0.124
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.004
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 Atoms1810
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing