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Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FO4 PBD Entry 1FO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Sitting Drop Batch Slide 7.5 293 12 mg/ml Xanthine Dehydrogenase (from Bovine Milk),
8 % Polyethylene Glycol 4000,
30 % Glycerol,
5 mM Dithiothreitol,
0.5 mM Sodium Salicylate,
0.2 m Ethylenediaminetetraacetic Acid,
16.65 mM Sodium Pyrophosphate (pH 8.5),
25 mM Potasium Phosphate (pH 6.5).
, Sitting Drop Batch Slide, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.573 α = 90 b = 124.37 β = 91.02 c = 148.177 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 210 2001-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.000 SPring-8 BL44B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 20 99.9 0.053 25.5 4.3 364190 363495 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.67 99.9 0.454 3.8 14437
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT shells PBD Entry 1FO4 1.65 20 363495 363267 4422 0.1772 0.1656 0.1962 0.1881 random shells
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] 1.543 -0.141 4.321 -5.864
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.54787 c_bond_d 0.010757
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19998 Nucleic Acid Atoms Solvent Atoms 1966 Heterogen Atoms 352
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing