3AM9

Complex of bovine xanthine dehydrogenase and trihydroxy FYX-051


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FO4PDB ENTRY 1FO4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429530%(wt/vol) glycerol, 50mM potassium phosphate buffer (pH 6.5) containing 8.0-9.5% polyethylene glycol 4000, 30% (wt/vol) glycerol, 0.2mM EDTA, 5mM DTT , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6253.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.916α = 90
b = 124.722β = 91.04
c = 146.195γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1Photon FactoryAR-NW12A

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
12.1733.440.0823151816144234
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)
2.172.280.312.78866

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FO42.1733.44151816144234758295.460.177060.173610.24302RANDOM28.148
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.611
r_dihedral_angle_4_deg18.76
r_dihedral_angle_3_deg16.459
r_dihedral_angle_1_deg6.951
r_scangle_it4.787
r_scbond_it3.136
r_angle_refined_deg2.099
r_angle_other_deg1.973
r_mcangle_it1.831
r_mcbond_it1.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.611
r_dihedral_angle_4_deg18.76
r_dihedral_angle_3_deg16.459
r_dihedral_angle_1_deg6.951
r_scangle_it4.787
r_scbond_it3.136
r_angle_refined_deg2.099
r_angle_other_deg1.973
r_mcangle_it1.831
r_mcbond_it1.051
r_chiral_restr0.144
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20068
Nucleic Acid Atoms
Solvent Atoms1914
Heterogen Atoms244

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling