7D0Q

Crystal structure of human HBO1-BRPF2 in complex with butyryl-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 Tris, pH 8.5, 20% w/v PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.4249.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.871α = 90
b = 39.599β = 122.89
c = 87.9γ = 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)R Merge 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
12.250.0199.30.09128.66.618377
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)
12.22.280.560.952.4

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 REPLACEMENTTHROUGHOUT5GK92.2150.011745292598.20.18890.1860.2435RANDOM69.279
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]
-2.87-0.92.390.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.867
r_sphericity_bonded37.881
r_sphericity_free35.277
r_dihedral_angle_4_deg21.888
r_dihedral_angle_3_deg17.598
r_rigid_bond_restr7.768
r_dihedral_angle_1_deg6.035
r_angle_refined_deg1.212
r_chiral_restr0.059
r_bond_refined_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.867
r_sphericity_bonded37.881
r_sphericity_free35.277
r_dihedral_angle_4_deg21.888
r_dihedral_angle_3_deg17.598
r_rigid_bond_restr7.768
r_dihedral_angle_1_deg6.035
r_angle_refined_deg1.212
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2480
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms59

Software

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