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SARS CoV-2 MAIN PROTEASE 3CLpro, ROOM TEMPERATURE, DAMAGE FREE XFEL MONOCLINIC STRUCTURE
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.5 293 12.5 % PEG 3350, 100 mmol/L bistris
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.6 α = 90 b = 55.4 β = 100.5 c = 45.6 γ = 90
Symmetry Space Group C 1 2 1
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 SLAC ePix10k 2020-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.26 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 MESH injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 40 (fs) 120 1 9.8 (KeV)
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 2.2 33 100 0.94 5 51 9428
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 2.2 2.3 0.18 1.77
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 FOURIER SYNTHESIS THROUGHOUT 6y2e 2.5 32.67 8961 467 93.16 0.17451 0.17227 0.1858 0.21719 0.2235 RANDOM 64.784
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] -1.56 0.96 -0.7 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.079 r_dihedral_angle_3_deg 20.553 r_dihedral_angle_4_deg 17.852 r_long_range_B_refined 14.02 r_long_range_B_other 13.935 r_mcangle_it 9.544 r_mcangle_other 9.541 r_scangle_other 9.529 r_dihedral_angle_1_deg 8.47 r_mcbond_it 6.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.079 r_dihedral_angle_3_deg 20.553 r_dihedral_angle_4_deg 17.852 r_long_range_B_refined 14.02 r_long_range_B_other 13.935 r_mcangle_it 9.544 r_mcangle_other 9.541 r_scangle_other 9.529 r_dihedral_angle_1_deg 8.47 r_mcbond_it 6.444 r_mcbond_other 6.444 r_scbond_other 6.207 r_scbond_it 6.206 r_angle_refined_deg 1.752 r_angle_other_deg 1.235 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling