1JRP

Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JRO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8295PEG, Tris, DTT, isopropanol at pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal Properties
Matthews coefficientSolvent content
3.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.617α = 109.59
b = 140.728β = 105.84
c = 157.665γ = 101.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.900NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
133099.10.15910.14.1135608135608-1000
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.10.7412.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JRO330-1000128790128790681899.070.1960.1960.1930.243RANDOM35.64
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]
1.7-0.370.01-2.65-1.92-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.078
r_scbond_it3.094
r_angle_refined_deg2.724
r_mcangle_it1.871
r_mcbond_it0.99
r_symmetry_hbond_refined0.395
r_nbd_refined0.219
r_xyhbond_nbd_refined0.195
r_chiral_restr0.151
r_bond_refined_d0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.078
r_scbond_it3.094
r_angle_refined_deg2.724
r_mcangle_it1.871
r_mcbond_it0.99
r_symmetry_hbond_refined0.395
r_nbd_refined0.219
r_xyhbond_nbd_refined0.195
r_chiral_restr0.151
r_bond_refined_d0.03
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms36348
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms400

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORphasing