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Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 PEG, Tris, DTT, isopropanol at pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal Properties Matthews coefficient Solvent content 3.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.875 α = 109.53 b = 141.053 β = 105.83 c = 158.113 γ = 101.33
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2001-02-14 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD CUSTOM-MADE 2001-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.100 NSLS X26C 2 SYNCHROTRON NSLS BEAMLINE X25 1.100 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 50 99.2 0.17 11.2 3.8 187987 187987 -1000
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.7 2.8 98 0.73 2.7
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-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FO4 2.7 50 178563 178563 9424 99.18 0.215 0.21505 0.21311 0.25154 RANDOM 39.67
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] 1.31 0.3 0.37 -1.57 -0.91 -0.03
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.576 r_scbond_it 3.409 r_angle_refined_deg 2.346 r_mcangle_it 2.03 r_mcbond_it 1.068 r_symmetry_hbond_refined 0.291 r_nbd_refined 0.177 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.142 r_bond_refined_d 0.025
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.576 r_scbond_it 3.409 r_angle_refined_deg 2.346 r_mcangle_it 2.03 r_mcbond_it 1.068 r_symmetry_hbond_refined 0.291 r_nbd_refined 0.177 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.142 r_bond_refined_d 0.025 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36348 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 360
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement