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Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 Double Mutant Y7F A9S bound to Cordycepin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F62 experimental model PDB 3EHD experimental model PDB 6EVS experimental model PDB 6QAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.1 M Bis-Tris Propane, pH 8.33, 21.429% PEG Smear High, 0.05 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.55 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.38 α = 90 b = 97.38 β = 90 c = 66.456 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS PILATUS3 6M 2023-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9700 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.77 84.33 99.64 0.181 0.191 0.059 0.991 5.9 9.8 68981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 92.21 1.052 1.153 0.459 0.158 0.2 5.8
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 1.77 42.17 1.96 64882 1930 93.98 0.187 0.186 0.1849 0.2158 0.2151
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 16.631 f_angle_d 0.892 f_chiral_restr 0.055 f_plane_restr 0.01 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4958 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHENIX phasing