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Crystal structure of Fab region of TAU-2212 neutralizing SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 309 26% (w/v) polyethylene glycol 3350, 0.2 M (NH4)2SO4, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.79 55.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.977 α = 90 b = 75.977 β = 90 c = 348.14 γ = 120
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 EIGER2 S 9M 2021-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.980 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.7 30 100 0.137 0.142 0.037 7.7 14.6 30854
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 2.7 2.75 100 0.904 0.937 0.243 0.916 14.1
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 (All) 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 7K8Q 2.705 29.746 30758 1554 99.673 0.204 0.2015 0.2015 0.2462 0.2462 RANDOM 93.79
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] 2.446 2.446 -4.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.087 r_dihedral_angle_3_deg 20.884 r_dihedral_angle_4_deg 19.081 r_lrange_it 11.351 r_dihedral_angle_1_deg 8.463 r_mcangle_it 6.379 r_scangle_it 6.027 r_mcbond_it 4.282 r_scbond_it 4.084 r_angle_refined_deg 0.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.087 r_dihedral_angle_3_deg 20.884 r_dihedral_angle_4_deg 19.081 r_lrange_it 11.351 r_dihedral_angle_1_deg 8.463 r_mcangle_it 6.379 r_scangle_it 6.027 r_mcbond_it 4.282 r_scbond_it 4.084 r_angle_refined_deg 0.969 r_symmetry_xyhbond_nbd_refined 0.357 r_symmetry_nbd_refined 0.307 r_nbtor_refined 0.303 r_nbd_refined 0.265 r_xyhbond_nbd_refined 0.249 r_ncsr_local_group_2 0.207 r_ncsr_local_group_1 0.192 r_chiral_restr 0.055 r_gen_planes_refined 0.019 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6293 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing Coot model building HKL-2000 data scaling HKL-2000 data reduction