7D0P

Crystal structure of human HBO1-BRPF2 in complex with propionyl-coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GK9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2890.1 M HEPES, pH 7.5, 12% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3948.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.679α = 90
b = 39.306β = 123.01
c = 87.744γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97892SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.850.019810.056.533222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.860.9525.4

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 REPLACEMENTTHROUGHOUT5GK91.850.0131519163897.680.17340.17080.2256RANDOM49.202
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]
-2.29-1.263.660.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.426
r_sphericity_free32.122
r_dihedral_angle_4_deg19.524
r_sphericity_bonded19.283
r_dihedral_angle_3_deg14.205
r_dihedral_angle_1_deg5.709
r_rigid_bond_restr5.656
r_angle_other_deg2.806
r_angle_refined_deg1.381
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.426
r_sphericity_free32.122
r_dihedral_angle_4_deg19.524
r_sphericity_bonded19.283
r_dihedral_angle_3_deg14.205
r_dihedral_angle_1_deg5.709
r_rigid_bond_restr5.656
r_angle_other_deg2.806
r_angle_refined_deg1.381
r_chiral_restr0.091
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2426
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing