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Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NADH Bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FO4 PDB 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 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.036 α = 90 b = 146.698 β = 106.03 c = 107.016 γ = 90
Symmetry Space Group P 1 21 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 4 2000-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
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 2.2 20 99.9 0.09 14.8 7.11 150203 149846 -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 2.2 2.24 99.9 0.377 3.64 3.7 7520
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 THROUGHOUT PDB Entry 1FO4 2.2 20 143758 141547 2211 0.198 0.1814 0.24 0.2212 Random
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 Key Refinement Restraint Deviation c_angle_deg 1.3 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20001 Nucleic Acid Atoms Solvent Atoms 1140 Heterogen Atoms 350
Software Software Software Name Purpose ADSC data collection EPMR phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling