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The crystal structure of RBD-Nanobody complex, DL4 (SA4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M0J 6M0J, 5M13 experimental model PDB 5M13 6M0J, 5M13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6 and 25% w/v Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.83 60.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.818 α = 90 b = 95.04 β = 90 c = 118.915 γ = 90
Symmetry Space Group P 2 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 PILATUS 6M-F 2021-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 1.75 36.58 100 0.112 0.117 0.033 0.998 14 12.8 91752 20
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 1.75 1.78 100 1.183 1.288 0.522 0.898 2.1 11.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6M0J, 5M13 1.75 36.58 1.34 91501 4580 99.78 0.1894 0.1879 0.2172 0.2262 29.19
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 22.0551 f_angle_d 0.8743 f_chiral_restr 0.0568 f_bond_d 0.0071 f_plane_restr 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4971 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 230
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction Aimless data scaling PHASER phasing