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Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M MMT (DL-malic acid, MES and Tris base in the molar ratios 1:2:2), pH 7.0, 25% PEG 1,500
Crystal Properties Matthews coefficient Solvent content 2.01 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.983 α = 90 b = 53.763 β = 101.242 c = 44.774 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 100 PIXEL DECTRIS PILATUS3 2M 2020-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.75 48.53 100 0.082 0.089 0.034 0.999 15 6.8 27173
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 100 0.967 0.387 0.747 2.1 7.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2BX4 1.75 48.53 27171 1309 99.971 0.174 0.1712 0.1811 0.2224 0.228 25.186
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] 0.636 -0.445 0.706 -1.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.02 r_dihedral_angle_3_deg 16.155 r_dihedral_angle_4_deg 15.211 r_dihedral_angle_1_deg 7.865 r_lrange_it 6.467 r_lrange_other 6.188 r_scangle_it 4.371 r_scangle_other 4.37 r_scbond_it 2.868 r_scbond_other 2.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.02 r_dihedral_angle_3_deg 16.155 r_dihedral_angle_4_deg 15.211 r_dihedral_angle_1_deg 7.865 r_lrange_it 6.467 r_lrange_other 6.188 r_scangle_it 4.371 r_scangle_other 4.37 r_scbond_it 2.868 r_scbond_other 2.866 r_mcangle_it 2.851 r_mcangle_other 2.85 r_mcbond_it 2.035 r_mcbond_other 2.028 r_angle_refined_deg 1.566 r_angle_other_deg 1.409 r_nbd_other 0.219 r_xyhbond_nbd_refined 0.211 r_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.193 r_symmetry_nbd_refined 0.186 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.17 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing