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Crystal structure of N-terminal SARS-CoV-2 nsp1 in complex with fragment hit 5E11 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 1.84 33.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.705 α = 90 b = 36.705 β = 90 c = 141.491 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 2021-07-08 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 0.96546 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) 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 1.15 32.58 96.64 0.997 9.77 8.8 35543
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 1.15 1.19 100 0.461 0.56 8
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 1.15 32.58 1.33 34385 868 96.64 0.193 0.1917 0.1913 0.2446 0.2397
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 19.402 f_angle_d 1.297 f_chiral_restr 0.103 f_bond_d 0.012 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 889 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data processing xia2 data reduction xia2 data scaling