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SARS-CoV-2 Omicron Variant Spike Glycoprotein Fusion Core (Q954H)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 20 mM 1,6-hexanediol; 20 mM 1 butanol; 20 mM 1,2-propanediol; 20 mM 2-propanol; 20 mM 1,4-butanediol; 20 mM 1,3-propanediol; 12.5% PEG1000; 12.5% PEG3350; 12.5% 2-methyl-2,4-pentanediol; 100 mM imidazole/MES monohydrate buffer (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.04 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.375 α = 90 b = 56.686 β = 90 c = 84.347 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 2022-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920078 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.119 84.347 92.5 0.21 0.997 6.2 7.3 12464 26.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.119 2.237 50.1 1.571 0.566 1.2 6.8
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 2.12 43.88 1.35 12435 1241 85.36 0.2191 0.2156 0.2154 0.2498 0.2501 41.45
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 15.1227 f_angle_d 0.5523 f_chiral_restr 0.0374 f_bond_d 0.0036 f_plane_restr 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1965 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement