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Rat Xanthine oxidoreductase, NADH bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 PEG 8000, HEPES, lithium sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.801 α = 90 b = 137.548 β = 90 c = 222.251 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 32.19 99.6 0.131 9.6 4.1 292799
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 1.787 1.813 1.396
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 4YTY 1.77 32.19 278050 14638 99.26 0.18922 0.1875 0.1962 0.22195 0.2296 RANDOM 25.314
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 34.418 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 14.247 r_dihedral_angle_1_deg 7.083 r_long_range_B_refined 4.908 r_long_range_B_other 4.908 r_scangle_other 4.022 r_mcangle_it 2.674 r_mcangle_other 2.674 r_scbond_it 2.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.418 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 14.247 r_dihedral_angle_1_deg 7.083 r_long_range_B_refined 4.908 r_long_range_B_other 4.908 r_scangle_other 4.022 r_mcangle_it 2.674 r_mcangle_other 2.674 r_scbond_it 2.651 r_scbond_other 2.651 r_mcbond_it 1.913 r_mcbond_other 1.911 r_angle_refined_deg 1.574 r_angle_other_deg 0.969 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 20004 Nucleic Acid Atoms Solvent Atoms 1099 Heterogen Atoms 242
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing