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SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 Peptide solution: Lyophilized TFA salt dissolved in 1% w/v beta-D-octylglucoside; HRN (4 mg/mL), HRC-QEYKKEKE (3 mg/mL)
Well solution: 0.1 M Tris pH 7.8, 26% w/v PEG3350, 0.3 M MgCl2
Drop: 1 uL peptide solution, 1 uL well solution
Reservoir: 150 uL in VDXm plate
Crystal Properties Matthews coefficient Solvent content 1.92 35.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.543 α = 90 b = 54.458 β = 90 c = 80.119 γ = 90
Symmetry Space Group P 21 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 EIGER X 9M 2020-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920087 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 80.12 99.5 0.088 0.096 0.038 0.999 9 6.5 12351 54.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.2 1.565 1.705 0.666 0.475 1.2 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6LXT 2.2 45.04 1.34 12313 1217 99.07 0.2463 0.2429 0.2485 0.2784 0.2874 88.63
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 19.2173 f_angle_d 0.3648 f_chiral_restr 0.0343 f_bond_d 0.0023 f_plane_restr 0.0011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1976 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data scaling Aimless data scaling PHASER phasing XDS data reduction