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Functional Implications of Hexameric Dynamics in SARS-CoV-2 Nsp15
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 7.5 298 100 mM HEPES-NaOH, pH 7.5, 200 mM calcium acetate, 8% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 5.11 75.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.2 α = 90 b = 154.2 β = 90 c = 116.2 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 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 fixed target
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 55068 48079 55068
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 0.98 6.8 420 31487 80.2
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 0.27 1.3
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 MOLECULAR REPLACEMENT FREE R-VALUE 3 29.64 29954 1544 99.87 0.16867 0.16741 0.1751 0.19318 0.1936 RANDOM 82.248
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] 0.52 0.26 0.52 -1.7
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.129 r_long_range_B_other 13.129 r_dihedral_angle_3_deg 12.072 r_scangle_other 10.785 r_mcangle_it 8.02 r_mcangle_other 8.02 r_scbond_it 7.078 r_scbond_other 7.077 r_dihedral_angle_1_deg 5.783 r_mcbond_it 5.353
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.129 r_long_range_B_other 13.129 r_dihedral_angle_3_deg 12.072 r_scangle_other 10.785 r_mcangle_it 8.02 r_mcangle_other 8.02 r_scbond_it 7.078 r_scbond_other 7.077 r_dihedral_angle_1_deg 5.783 r_mcbond_it 5.353 r_mcbond_other 5.34 r_angle_refined_deg 0.929 r_angle_other_deg 0.348 r_chiral_restr 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5492 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB-REDO refinement CrystFEL data reduction XDS data scaling MOLREP phasing