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Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M0J 6M0j, 7jx3 experimental model PDB 7JX3 6M0j, 7jx3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.09 M Buffer System 3 pH 8.5 contains Tris (base); BICINE
27% Precipitant Mix 2 contains Ethylene glycol and PEG8000
0.1 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.76 67.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.98 α = 90 b = 186.58 β = 96.4 c = 194.52 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2020-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.78 48.95 94.8 0.506 0.545 0.202 0.97 3.3 7.2 131453
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.78 2.83 99.8 3.26 3.671 1.641 0.18 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6M0j, 7jx3 2.78 48.9 122372 6375 92.9 0.2921 0.2904 0.2915 0.3247 0.3257 RANDOM 86.099
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] -1.9 0.79 4.32 -2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.543 r_dihedral_angle_3_deg 14.49 r_dihedral_angle_4_deg 13.66 r_dihedral_angle_1_deg 5.361 r_angle_refined_deg 0.668 r_chiral_restr 0.056 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25898 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 347
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction