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Crystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in complex with hypoxanthine
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 8.3 7.5 MM BACL2, 8% PEG 8000, 100 MM TRIS-HCL PH 8.3, 25 MM DTT AND 3% ISOPROPANOL
Crystal Properties Matthews coefficient Solvent content 3.34 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.77 α = 109.33 b = 139.94 β = 106.15 c = 158.04 γ = 101.05
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 MARMOSAIC 225 mm CCD 2008-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.7 51.03 98.2 0.14 6.4 1.97 183839
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 2.7 2.72 97.7 0.86 0.84 1.97
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 2.9 51.23 141476 7476 98.2 0.242 0.24 0.2398 0.281 0.2803 RANDOM 53.09
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] 1.29 0.48 -1.7 -0.3 -1.69 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.616 r_dihedral_angle_4_deg 17.077 r_dihedral_angle_3_deg 16.407 r_dihedral_angle_1_deg 4.839 r_angle_refined_deg 0.983 r_scangle_it 0.772 r_scbond_it 0.457 r_mcangle_it 0.41 r_mcbond_it 0.219 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.616 r_dihedral_angle_4_deg 17.077 r_dihedral_angle_3_deg 16.407 r_dihedral_angle_1_deg 4.839 r_angle_refined_deg 0.983 r_scangle_it 0.772 r_scbond_it 0.457 r_mcangle_it 0.41 r_mcbond_it 0.219 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 81 Heterogen Atoms 400
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing