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Crystal structure of N-terminal SARS-CoV-2 nsp1 in complex with fragment hit 11A7_AL6 refined against the anomalous diffraction data
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8A55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291.15 The crystallisation condition used is Index 71 (Cat. No.: HR2-944-71; Hampton Research, Aliso Viejo, CA, USA) containing 0.1 M BIS-TRIS pH 6.5, 0.2 M NaCl and 25% w/v Polyethylene glycol 3350.
Crystal Properties Matthews coefficient Solvent content 1.82 32.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.834 α = 90 b = 36.834 β = 90 c = 140.874 γ = 90
Symmetry Space Group P 43 21 2
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 2023-07-22 M SINGLE WAVELENGTH 2 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2023-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1 2 SYNCHROTRON DIAMOND BEAMLINE I23 2.75520 Diamond I23
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 1.12 35.64 98 0.084 0.086 0.018 0.997 12.1 21.7 37308
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.125 1.144 3.048 3.138 0.73 0.538 18
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.12 35.64 1.33 37093 1891 97.42 0.1955 0.1926 0.1945 0.2484 0.2426
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.867 f_angle_d 1.25 f_chiral_restr 0.097 f_plane_restr 0.014 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 920 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction