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Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JRO
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 = 92.617 α = 109.59 b = 140.728 β = 105.84 c = 157.665 γ = 101.25
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 2001-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.900 NSLS X4A
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 3 30 99.1 0.159 10.1 4.1 135608 135608 -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 3 3.1 0.741 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JRO 3 30 -1000 128790 128790 6818 99.07 0.196 0.196 0.193 0.243 RANDOM 35.64
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 -0.37 0.01 -2.65 -1.92 -0.47
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.078 r_scbond_it 3.094 r_angle_refined_deg 2.724 r_mcangle_it 1.871 r_mcbond_it 0.99 r_symmetry_hbond_refined 0.395 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.151 r_bond_refined_d 0.03
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.078 r_scbond_it 3.094 r_angle_refined_deg 2.724 r_mcangle_it 1.871 r_mcbond_it 0.99 r_symmetry_hbond_refined 0.395 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.151 r_bond_refined_d 0.03 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36348 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 400
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building REFMAC refinement X-PLOR phasing