Navigation Tabs Room temperature structure of NSP15 Endoribonuclease from SARS CoV-2 solved using SFX.
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.5 295 NendoU protein 75 mg/ml (20 mM HEPES pH 7.5, 150mM NaCl, 1mM TCEP) is added to the precipitant solution (100mM Na Citrate pH 5.5, 20% PEG 1000, 20% 2-Methyl-2,4-pentanediol (MPD)) in a 1:7 protein:precipitant ratio with agitation at 295K overnight.
Crystal Properties Matthews coefficient Solvent content 5.11 75.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154 α = 90 b = 154 β = 90 c = 117 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 295 PIXEL SLAC ePix10k 2M 2020-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.277 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 30 (fs) 120 undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 25066
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 MESH injector undefined (µl/min) undefined (µm)
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 2.6 33.67 100 0.94 3.1 101 48524
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 2.6 2.69 100 0.03 0.2 70
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 6xdh 2.6 33.67 45981 2503 99.9 0.19229 0.19137 0.2 0.20877 0.22 RANDOM 47.684
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] -8.54 -8.54 17.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_4_deg 13.657 r_dihedral_angle_1_deg 5.347 r_long_range_B_refined 1.278 r_long_range_B_other 1.278 r_angle_refined_deg 1.034 r_angle_other_deg 0.909 r_mcangle_it 0.829 r_mcangle_other 0.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_3_deg 14.785 r_dihedral_angle_4_deg 13.657 r_dihedral_angle_1_deg 5.347 r_long_range_B_refined 1.278 r_long_range_B_other 1.278 r_angle_refined_deg 1.034 r_angle_other_deg 0.909 r_mcangle_it 0.829 r_mcangle_other 0.829 r_scangle_other 0.502 r_mcbond_it 0.458 r_mcbond_other 0.458 r_scbond_it 0.267 r_scbond_other 0.266 r_chiral_restr 0.06 r_bond_refined_d 0.006 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 5504 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction Aimless data scaling MOLREP phasing
