☰ Navigation Tabs
Nanobody bound SARS-CoV-2 Nsp9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KRI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 1.8M ammonium sulfate, 0.1M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.19 61.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.025 α = 90 b = 165.025 β = 90 c = 46.002 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 EIGER X 16M 2022-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.45 47.6 95.3 0.042 0.998 10.6 3.6 25484 57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.58 0.66 0.409 1.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7KRI 2.45003185971 40.1795060787 1.34496889735 25462 1252 95.0713165559 0.204449597035 0.203177800088 0.2091 0.228865459827 0.2342 82.1645754963
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 24.75 f_angle_d 1.5024 f_chiral_restr 0.1046 f_bond_d 0.0209 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3088 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing