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Crystal structure of Cryo2RT SARS-CoV-2 main protease at 294K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7GRR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 300 mM sodium nitrate, 300 mM disodium hydrogen phosphate, 300 mM ammonium sulphate, 100 mM MES/imidazole pH 6.5, 10% (w/v) PEG550 MME and 20% (w/v) PEG 20K
Crystal Properties Matthews coefficient Solvent content 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.64 α = 90 b = 101.558 β = 90 c = 105.255 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 294 PIXEL DECTRIS PILATUS 6M 2024-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.9795 ESRF BM07
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.28 73.09 99.4 0.143 0.99 7.91 5.2 33990
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.42 99.4 1.13 0.63 1.44 5.39
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 THROUGHOUT 2.282 73.08 33920 1603 99.5 0.2049 0.203 0.1946 0.2441 0.2383 RANDOM 50.2
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] 6.8762 -6.2409 -0.6353
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.09 t_omega_torsion 3.3 t_angle_deg 0.94 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.09 t_omega_torsion 3.3 t_angle_deg 0.94 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4676 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 31
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing