3BPT | pdb_00003bpt

Crystal structure of human beta-hydroxyisobutyryl-CoA hydrolase in complex with quercetin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MATRIX SEEDING5.52930.1M Citrate pH 5.5, 20% PEG 3350, 5mM Quercetin added to the protein, MATRIX SEEDING, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.096α = 90
b = 76.642β = 108.24
c = 55.789γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97912SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.531.0583.30.0730.044176.646971446132
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5831.80.3770.3561.52.22591

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.5314461344613233483.280.149090.146590.14530.196780.1924RANDOM10.639
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]
0.38-0.87-0.18-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.219
r_dihedral_angle_4_deg12.581
r_dihedral_angle_3_deg12.045
r_scangle_it8.108
r_dihedral_angle_1_deg5.823
r_scbond_it5.819
r_mcangle_it3.584
r_mcbond_it2.469
r_angle_refined_deg1.594
r_angle_other_deg0.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.219
r_dihedral_angle_4_deg12.581
r_dihedral_angle_3_deg12.045
r_scangle_it8.108
r_dihedral_angle_1_deg5.823
r_scbond_it5.819
r_mcangle_it3.584
r_mcbond_it2.469
r_angle_refined_deg1.594
r_angle_other_deg0.981
r_mcbond_other0.822
r_chiral_restr0.099
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2803
Nucleic Acid Atoms
Solvent Atoms587
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
SHELXDphasing