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Rat Xanthine oxidoreductase, D428A variant, NADH bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 295 9-11% polyethylene glycol 8000, 0.6M Li2SO4, 5mM DTT, 1mM sodium salicylate, 0.4mM EDTA, 15% glycerol, 40mM HEPES (pH 6.20), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.718 α = 90 b = 138.334 β = 90 c = 222.513 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 1.8 49.36 99.1 0.056 21.8 3.6 282210
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 1.8 1.842 0.215
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 3AN1 1.8 49.36 273512 8587 99.67 0.16525 0.16421 0.1755 0.19829 0.2068 RANDOM 21.373
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 33.94 r_dihedral_angle_4_deg 17.869 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_1_deg 7.041 r_long_range_B_refined 5.038 r_long_range_B_other 5.038 r_scangle_other 4.174 r_scbond_it 2.82 r_scbond_other 2.82 r_mcangle_it 2.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.94 r_dihedral_angle_4_deg 17.869 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_1_deg 7.041 r_long_range_B_refined 5.038 r_long_range_B_other 5.038 r_scangle_other 4.174 r_scbond_it 2.82 r_scbond_other 2.82 r_mcangle_it 2.732 r_mcangle_other 2.732 r_mcbond_it 1.986 r_mcbond_other 1.986 r_angle_refined_deg 1.73 r_angle_other_deg 1.047 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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 20016 Nucleic Acid Atoms Solvent Atoms 1347 Heterogen Atoms 242
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing