7D0S

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2890.2 M L-Proline, 0.1 M HEPES, pH 7.5, 24% w/v PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.4449.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.098α = 90
b = 39.565β = 122.88
c = 88.328γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9792SSRFBL17U

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
12.350.0194.70.1123.35.816040
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)
12.32.380.772.73.6

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 REPLACEMENTTHROUGHOUT5GK92.350.011515777295.060.21550.21330.2565RANDOM63.503
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]
-3.35-0.755.73-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.104
r_sphericity_bonded24.215
r_dihedral_angle_4_deg22.528
r_rigid_bond_restr19.654
r_dihedral_angle_3_deg17.348
r_dihedral_angle_1_deg6.124
r_angle_refined_deg1.44
r_angle_other_deg0.992
r_chiral_restr0.084
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.104
r_sphericity_bonded24.215
r_dihedral_angle_4_deg22.528
r_rigid_bond_restr19.654
r_dihedral_angle_3_deg17.348
r_dihedral_angle_1_deg6.124
r_angle_refined_deg1.44
r_angle_other_deg0.992
r_chiral_restr0.084
r_bond_refined_d0.011
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2417
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing