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PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment D04 from the F2X-Entry Screen in orthorhombic space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BB2
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 2.59 52.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.05 α = 90 b = 99.28 β = 90 c = 103.5 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 100 PIXEL DECTRIS PILATUS3 6M 2022-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2 45.89 99.9 0.154 0.17 0.997 8.99 48244
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 2 2.12 99.9 1.48 1.631 0.47
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 45.89 46143 2101 99.82 0.21169 0.20975 0.2165 0.25461 0.2607 RANDOM 35.174
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] -1.28 1.97 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.935 r_dihedral_angle_4_deg 20.126 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_1_deg 7.506 r_long_range_B_other 7.002 r_long_range_B_refined 6.997 r_scangle_other 4.881 r_mcangle_it 3.784 r_mcangle_other 3.784 r_scbond_it 3.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.935 r_dihedral_angle_4_deg 20.126 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_1_deg 7.506 r_long_range_B_other 7.002 r_long_range_B_refined 6.997 r_scangle_other 4.881 r_mcangle_it 3.784 r_mcangle_other 3.784 r_scbond_it 3.099 r_scbond_other 3.098 r_mcbond_it 2.46 r_mcbond_other 2.459 r_angle_refined_deg 1.494 r_angle_other_deg 1.334 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4709 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing