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Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus in Complex with Bound Inhibitor Pterin-6-aldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JRO PDB ENTRY 1JRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 100 MM TRIS PH 8.3, 6-8 % PEG 8000, 6-8 MM BACL, 5-25 MM DTT, 3-4 % ISOPROPANOL, 10-15 MG/ML PROTEIN, HANGING DROP VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3.35 63.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.571 α = 109.63 b = 140.695 β = 105.83 c = 157.859 γ = 101.23
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 CCD A DOUBLY FOCUSING TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C NSLS X26C
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 3.3 50 99.1 0.18 8.9 4 102161
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 3.3 3.36 98.6 0.65 2.6 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (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 1JRO 3.3 50 96884 5185 99.1 0.188 0.186 0.1926 0.224 0.2291 RANDOM 23.23
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] 1.22 -0.28 -0.5 -2.26 -1.87 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.299 r_dihedral_angle_3_deg 16.858 r_dihedral_angle_4_deg 15.664 r_dihedral_angle_1_deg 4.79 r_angle_refined_deg 0.992 r_scangle_it 0.68 r_scbond_it 0.378 r_mcangle_it 0.204 r_mcbond_it 0.098 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.299 r_dihedral_angle_3_deg 16.858 r_dihedral_angle_4_deg 15.664 r_dihedral_angle_1_deg 4.79 r_angle_refined_deg 0.992 r_scangle_it 0.68 r_scbond_it 0.378 r_mcangle_it 0.204 r_mcbond_it 0.098 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36372 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 416
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing