☰ Navigation Tabs
Structure of the SARS-CoV-2 Spike N-terminal domain(NTD) in complex with the BLN8 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% w/v Polyethylene glycol 6,000, 0.1 M Sodium iodide
Crystal Properties Matthews coefficient Solvent content 3.32 62.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.94 α = 110.914 b = 117.493 β = 90.274 c = 138.049 γ = 96.371
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 EIGER2 S 9M 2024-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97925 SSRF BL02U1
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 3.13 64.4 98.6 0.909 5.1 3.4 73865 37.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.13 3.21 0.486
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 3.13 64.4 1.97 73689 3606 98.38 0.2341 0.2315 0.2316 0.2849 0.2851 45.99
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 11.6128 f_angle_d 0.5982 f_chiral_restr 0.0449 f_plane_restr 0.0045 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21911 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 472
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing