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nsp14 of SARS-CoV-2 in complex with a camelid nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DIY for nsp14 experimental model PDB 8R2V for nsp14 in silico model AlphaFold for vhh
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 22,5-26,25% w/v PEG 3350, 0.1 M Bis Tris propane, 0.2 M sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.03 39.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.514 α = 90 b = 80.801 β = 90 c = 138.117 γ = 90
Symmetry Space Group P 21 21 21
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 2023-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
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 2.267 69.743 93.2 0.134 0.14 0.041 0.999 10.4 12 209521 49.4
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 2.267 2.537 1.735 1.822 0.55 0.755
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.267 69.74 17517 881 59.2 0.2361 0.2333 0.2897 0.2937 RANDOM 50.4
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] -0.4175 1.7766 -1.3592
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.37 t_omega_torsion 2.85 t_angle_deg 0.91 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4506 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 3
Software Software Software Name Purpose autoPROC data reduction autoPROC data scaling PHASER phasing ISOLDE model building BUSTER refinement