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The crystal structure of Nsp9 RNA binding protein of SARS CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 1.8 M di-Ammonium hydrogen citrate,
0.1 M Sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.02 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.883 α = 90 b = 89.883 β = 90 c = 132.587 γ = 120
Symmetry Space Group P 61 2 2
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 PILATUS3 S 6M 2020-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97919 APS 19-BM
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 2.9 45 97.1 0.19 0.199 0.058 0.987 17.4 12 7299 -3 99.12
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 2.9 2.95 79 1.753 1.874 0.646 0.452 1.09 6.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1UW7 2.95 44.94 1.35 6932 341 97.09 0.2417 0.2398 0.2473 0.276 0.2831 random 123.76
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 14.7664 f_angle_d 0.6973 f_chiral_restr 0.0394 f_plane_restr 0.0046 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1685 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SBC-Collect data collection PHENIX refinement HKL-3000 data scaling MOLREP phasing HKL-3000 data reduction