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Rat Xanthine oxidoreductase, NAD bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 PEG 8000, HEPES, lithium formate, pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.353 α = 90 b = 137.663 β = 90 c = 221.969 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2017-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
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 1.77 30.57 99.8 0.117 1.34 4.1 291681
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 1.77 1.83 99.2 1.672
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 1WYG 1.77 30.57 276993 14567 99.84 0.20083 0.19895 0.2068 0.23661 0.2428 RANDOM 28.44
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 r_dihedral_angle_2_deg 34.914 r_long_range_B_refined 23.109 r_long_range_B_other 22.653 r_dihedral_angle_4_deg 16.669 r_dihedral_angle_3_deg 14.802 r_dihedral_angle_1_deg 7.015 r_scangle_other 4.204 r_mcangle_it 2.938 r_mcangle_other 2.938 r_scbond_it 2.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.914 r_long_range_B_refined 23.109 r_long_range_B_other 22.653 r_dihedral_angle_4_deg 16.669 r_dihedral_angle_3_deg 14.802 r_dihedral_angle_1_deg 7.015 r_scangle_other 4.204 r_mcangle_it 2.938 r_mcangle_other 2.938 r_scbond_it 2.801 r_scbond_other 2.801 r_mcbond_it 2.058 r_mcbond_other 2.058 r_angle_refined_deg 1.506 r_angle_other_deg 0.952 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20047 Nucleic Acid Atoms Solvent Atoms 1592 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling EPMR phasing