5GK9

Crystal structure of human HBO1 in complex with BRPF2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP289Tacsimate Tris-HCl, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4148.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.47α = 90
b = 39.321β = 122.1
c = 87.666γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9786SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.45097.90.078183.714322
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)
12.42.4997.90.5223.63.7

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 REPLACEMENTTHROUGHOUT2GIV2.4501359372997.690.260.2330.26RANDOM49.289
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]
-2.56-0.283.84-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.76
r_dihedral_angle_3_deg21.347
r_dihedral_angle_4_deg19.861
r_dihedral_angle_1_deg7.492
r_angle_refined_deg1.777
r_angle_other_deg0.954
r_chiral_restr0.234
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.76
r_dihedral_angle_3_deg21.347
r_dihedral_angle_4_deg19.861
r_dihedral_angle_1_deg7.492
r_angle_refined_deg1.777
r_angle_other_deg0.954
r_chiral_restr0.234
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2403
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms52

Software

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