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Crystal structure of tick-borne encephalitis virus methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 289 PEG 8000, glycerol
Crystal Properties Matthews coefficient Solvent content 2.33 47.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.027 α = 79.66 b = 49.468 β = 82.78 c = 85.274 γ = 77.07
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2017-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
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 1.89 47.62 88.1 0.057 0.081 0.057 0.991 8.8 1.9 38316 23.79
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 1.89 1.94 84.7 0.368 0.521 0.368 0.639 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OXT 1.894 38.84 1.96 38258 1891 87.94 0.2248 0.2225 0.2706 0.2875 28.9785
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 11.443 f_angle_d 0.922 f_chiral_restr 0.061 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3998 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XSCALE data reduction PHENIX phasing