☰ Navigation Tabs
Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 10% (v/v) MPD, 0.1M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 4.44 72.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.067 α = 90 b = 168.067 β = 90 c = 52.304 γ = 120
Symmetry Space Group P 31 2 1
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 2020-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 30.002 99.9 0.13 0.13 0.13 0.042 0.997 13.6 20.02 78401 34.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.867 100 1.656 1.658 1.698 0.3742 0.707 1.35 18.7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3r24 1.8 30.002 78401 3909 99.972 0.154 0.152 0.152 0.188 0.1879 43.686
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] -0.342 -0.171 -0.342 1.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.896 r_dihedral_angle_4_deg 17.672 r_dihedral_angle_3_deg 14.392 r_scangle_it 9.964 r_scbond_it 8.785 r_lrange_it 8.725 r_mcangle_it 7.228 r_rigid_bond_restr 6.541 r_dihedral_angle_1_deg 6.316 r_mcbond_it 6.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.896 r_dihedral_angle_4_deg 17.672 r_dihedral_angle_3_deg 14.392 r_scangle_it 9.964 r_scbond_it 8.785 r_lrange_it 8.725 r_mcangle_it 7.228 r_rigid_bond_restr 6.541 r_dihedral_angle_1_deg 6.316 r_mcbond_it 6.118 r_angle_refined_deg 1.851 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.126 r_chiral_restr 0.124 r_bond_refined_d 0.015 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3163 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing