Navigation Tabs Oxidized form of SARS-CoV-2 Main Protease determined by XFEL radiation
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 291 Vapor diffusion was set up with 2 uL MPro (35 mg/mL) and 2 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO. Seedstock was prepared by 100 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO and 4 uL seeds from plate, vortex 5 times for 5 seconds, add 12.5 uL of MPro (35 mg/mL) and incubate at 18 deg overnight. Final sample was prepared in batch mode by adding 900 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO and 100 uL seedstock and 100 uL MPro (35 mg per mL). Add seedbeads (250 uL volume in 1.5 mL Eppi) and incubate overnight at 900 rpm and 18 deg. Crystals were soaked with crystallization buffer containing containing 4 mM Calpeptin.
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.4 α = 90 b = 104.4 β = 90 c = 68.7 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL AGIPD 2021-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE SPB/SFX 1.3 European XFEL SPB/SFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 GDVN injection
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 GDVN undefined (µl/min) undefined (µm)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 2.2 32.63 99.99 0.9785 0.1693 7.41 355.55 38870 28.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.218 2.257 99.89 0.29 1.213 1.07 20.3
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 R-Free Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7AKU 2.25 24.61 36338 1016 99.98 0.1779 0.1761 0.2433
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4608 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing