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Crystal structure of xanthine dehydrogenase family protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.94 68.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.86 α = 90 b = 126.792 β = 90 c = 294.49 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 80 CCD Nonius Kappa CCD 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.43 147.24 96 0.87 1.1 12.2 56814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.43 3.55 0.512
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 3.44 147.24 50560 2706 93.67 0.2894 0.2875 0.2857 0.326 0.3248 RANDOM 67.87
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] -0.09 -0.78 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.891 r_dihedral_angle_3_deg 18.986 r_dihedral_angle_4_deg 14.895 r_dihedral_angle_1_deg 8.895 r_rigid_bond_restr 3.928 r_sphericity_bonded 2.615 r_angle_refined_deg 1.388 r_chiral_restr 0.097 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18466 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 212
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing