7D0R

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2890.03 M Citric acid, 0.07 M BIS-TRIS propane, pH 7.6, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4349.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.345α = 90
b = 39.636β = 123.24
c = 88.096γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9790SSRFBL17U

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
11.9550.0197.80.070.9938.56.226858
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)
11.952.020.70.892.3

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 REPLACEMENTTHROUGHOUT5GK91.9550.0125279136197.830.18480.18240.2308RANDOM53.543
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]
-1.5-0.282.75-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.543
r_sphericity_bonded32.274
r_sphericity_free30.123
r_dihedral_angle_3_deg15.614
r_dihedral_angle_4_deg12.878
r_dihedral_angle_1_deg5.803
r_rigid_bond_restr3.986
r_angle_refined_deg1.403
r_angle_other_deg1.301
r_chiral_restr0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.543
r_sphericity_bonded32.274
r_sphericity_free30.123
r_dihedral_angle_3_deg15.614
r_dihedral_angle_4_deg12.878
r_dihedral_angle_1_deg5.803
r_rigid_bond_restr3.986
r_angle_refined_deg1.403
r_angle_other_deg1.301
r_chiral_restr0.32
r_gen_planes_refined0.013
r_gen_planes_other0.013
r_bond_refined_d0.009
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2434
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms58

Software

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