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Structural Asymmetry in SARS-CoV-2 Nsp15 Hexamer Important for Catalytic Activity
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 277 100 mM HEPES-NaOH, pH 7.5, 200 mM calcium acetate, 8% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 5.2 76.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.7 α = 90 b = 116.6 β = 119.4 c = 154.8 γ = 90
Symmetry Space Group P 1 21 1
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 PSI JUNGFRAU 4M 2023-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.075 ESRF ID29
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 foil-on-foil fixed-target delivery system fixed target
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 54091 48081 54091
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 30 100 0.93 3.6 280 96013 85.9
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 3.11 0.08 0.54
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3 29.98 1.33 96013 4632 99.95 0.1979 0.1855 0.1801 0.2108 0.2018 0.05 76
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 12.244 f_angle_d 0.443 f_chiral_restr 0.043 f_plane_restr 0.003 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16476 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement REFMAC refinement PDB-REDO refinement CrystFEL data reduction XDS data scaling MOLREP phasing