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PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment D08 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 = 112.35 α = 90 b = 53.06 β = 102.21 c = 44.81 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 1.7 47.82 99.8 0.071 0.079 0.9990000000000001 13.63 28467
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 1.7 1.8 99.8 1.53 1.6840000000000002 0.48100000000000004
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 1.7 47.82 27042 1424 99.86 0.19985 0.19817 0.2054 0.23256 0.2395 RANDOM 31.08
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] 0.97 0.03 -0.33 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.399 r_dihedral_angle_4_deg 15.214 r_dihedral_angle_3_deg 14.307 r_dihedral_angle_1_deg 7.935 r_long_range_B_refined 7.053 r_long_range_B_other 7.052 r_scangle_other 5.424 r_scbond_it 3.676 r_scbond_other 3.675 r_mcangle_it 3.637
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.399 r_dihedral_angle_4_deg 15.214 r_dihedral_angle_3_deg 14.307 r_dihedral_angle_1_deg 7.935 r_long_range_B_refined 7.053 r_long_range_B_other 7.052 r_scangle_other 5.424 r_scbond_it 3.676 r_scbond_other 3.675 r_mcangle_it 3.637 r_mcangle_other 3.636 r_mcbond_it 2.607 r_mcbond_other 2.607 r_angle_refined_deg 1.617 r_angle_other_deg 1.409 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 2393 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing