1JRO

Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus


X-RAY DIFFRACTION

Starting Model(s)

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

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 = 92.875α = 109.53
b = 141.053β = 105.83
c = 158.113γ = 101.33
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-02-14MSINGLE WAVELENGTH
21x-ray100CCDCUSTOM-MADE2001-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.100NSLSX26C
2SYNCHROTRONNSLS BEAMLINE X251.100NSLSX25

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
1,22.75099.20.1711.23.8187987187987-1000
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)
1,22.72.8980.732.7

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1FO42.750178563178563942499.180.2150.215050.213110.25154RANDOM39.67
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]
1.310.30.37-1.57-0.91-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.576
r_scbond_it3.409
r_angle_refined_deg2.346
r_mcangle_it2.03
r_mcbond_it1.068
r_symmetry_hbond_refined0.291
r_nbd_refined0.177
r_xyhbond_nbd_refined0.177
r_chiral_restr0.142
r_bond_refined_d0.025
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.576
r_scbond_it3.409
r_angle_refined_deg2.346
r_mcangle_it2.03
r_mcbond_it1.068
r_symmetry_hbond_refined0.291
r_nbd_refined0.177
r_xyhbond_nbd_refined0.177
r_chiral_restr0.142
r_bond_refined_d0.025
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms36348
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms360

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement