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Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction intermediate derived from the crystal soaked into the solution at pH 4.0 under 277 K for 24 hourss
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XWC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 sodium cacodylate, PEG 4000, MgCl2
Crystal Properties Matthews coefficient Solvent content 2.03 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.873 α = 90 b = 69.404 β = 90 c = 88.67 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 EIGER X 16M 2022-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.04 Photon Factory BL-1A
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 1.68 46.18 99.9 0.997 8.3 6.6 44239 16.83
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 1.68 1.71 0.514
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.68 46.18 1.34 44163 2160 99.82 0.1711 0.1689 0.1684 0.2135 0.2127 21.03
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 f_dihedral_angle_d 23.0316 f_angle_d 1.656 f_chiral_restr 0.0647 f_bond_d 0.0152 f_plane_restr 0.0121
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2491 Nucleic Acid Atoms 471 Solvent Atoms 378 Heterogen Atoms 184
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing