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PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment B07 from the F2X-Entry Screen in monoclinic space group
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 VAPOR DIFFUSION, SITTING DROP 7.7 291 0.2 M MIB (sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3) pH 7.7, 23.5 % PEG 1500, 5 % DMSO, 1 mM DTT. Crystal seeds were used to ensure reproducible crystal growth.
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.4 α = 90 b = 53.09 β = 102.58 c = 44.41 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 2022-04-22 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) 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 1.52 47.91 99.2 0.081 0.08900000000000001 0.9990000000000001 12.91 39439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.61 98.4 1.7730000000000001 1.944 0.486
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 1.52 47.91 37466 1972 99.26 0.2045 0.20293 0.2117 0.23494 0.243 RANDOM 25.958
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] 1.52 -0.43 0.25 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.617 r_dihedral_angle_1_deg 7.241 r_dihedral_angle_2_deg 5.835 r_long_range_B_other 5.779 r_long_range_B_refined 5.774 r_scangle_other 4.528 r_scbond_it 3.264 r_scbond_other 3.263 r_mcangle_it 2.975 r_mcangle_other 2.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.617 r_dihedral_angle_1_deg 7.241 r_dihedral_angle_2_deg 5.835 r_long_range_B_other 5.779 r_long_range_B_refined 5.774 r_scangle_other 4.528 r_scbond_it 3.264 r_scbond_other 3.263 r_mcangle_it 2.975 r_mcangle_other 2.975 r_mcbond_it 2.238 r_mcbond_other 2.231 r_angle_refined_deg 1.596 r_angle_other_deg 0.55 r_chiral_restr 0.079 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2406 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing