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Crystal structure of N-terminal SARS-CoV-2 nsp1 in complex with fragment hit 11C6 refined against 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 291.15 0.1 M BIS-TRIS pH 6.5, 0.2 M NaCl and 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 1.83 32.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.817 α = 90 b = 36.817 β = 90 c = 141.205 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 2021-08-29 M SINGLE WAVELENGTH 2 1 x-ray 45 PIXEL DECTRIS PILATUS 12M 2023-02-01 M SINGLE WAVELENGTH 3 1 x-ray 45 PIXEL DECTRIS PILATUS 12M 2023-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1 2 SYNCHROTRON DIAMOND BEAMLINE I23 2.75 Diamond I23 3 SYNCHROTRON DIAMOND BEAMLINE I23 4.5 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.417 35.63 99.6 0.019 1 18.3 7.1 19328
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.417 1.442 0.276 0.816 2.2
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 1.42 35.63 1.34 19314 958 99.5 0.1797 0.1785 0.179 0.2028 0.204
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 10.041 f_angle_d 1.278 f_chiral_restr 0.084 f_plane_restr 0.016 f_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 910 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling autoPROC data processing