☰ Navigation Tabs
SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JYV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.9 M Ammonium Sulfate, 20 mM Magnesium chloride, 0.1M Bis-tris propane, 2% Ethylene glycol, 2% 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.31 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.812 α = 106.53 b = 64.467 β = 92.43 c = 76.422 γ = 97.51
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 16M 2021-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953739 Australian Synchrotron MX2
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 2.3 48.22 95.4 0.084 0.112 0.074 0.993 4.1 2 37380 40.65
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 2.3 2.38 95.5 0.639 0.864 0.578 0.54 2.1
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 7JYV 2.3 41.29 37369 1826 95.4 0.195 0.192 0.204 0.238 0.2585 RANDOM 48.68
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] 4.1158 2.0199 -7.4203 18.2741 0.9895 -22.3899
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.26 t_omega_torsion 3.28 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.26 t_omega_torsion 3.28 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6284 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 29
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction