4YTY

Structure of rat xanthine oxidoreductase, C535A/C992R/C1324S, NADH bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AN1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2293PEG 8000, lithium formate, DTT, sodium salicylate, EDTA, glycerol, HEPES
Crystal Properties
Matthews coefficientSolvent content
2.6453.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.988α = 90
b = 137.404β = 90
c = 222.705γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2008-12-09MSINGLE 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)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
12.249.599.718.27.4153088

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 REPLACEMENTTHROUGHOUT3AN12.249.5145410767899.650.180.17780.2211RANDOM21.237
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.404
r_dihedral_angle_4_deg16.898
r_dihedral_angle_3_deg14.121
r_dihedral_angle_1_deg6.092
r_scangle_it2.567
r_scbond_it1.592
r_angle_refined_deg1.294
r_mcangle_it1.033
r_mcbond_it0.643
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.404
r_dihedral_angle_4_deg16.898
r_dihedral_angle_3_deg14.121
r_dihedral_angle_1_deg6.092
r_scangle_it2.567
r_scbond_it1.592
r_angle_refined_deg1.294
r_mcangle_it1.033
r_mcbond_it0.643
r_nbtor_refined0.299
r_nbd_refined0.192
r_symmetry_vdw_refined0.153
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.122
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20071
Nucleic Acid Atoms
Solvent Atoms1407
Heterogen Atoms256

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata reduction
SCALEPACKdata scaling
MOLREPphasing