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X-ray Crystallographic Structure of Orf9b from SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 Protein at 8.3 mg/ml in 20 mM Tris pH 7.0
150 mM NaCl, 1mM DTT was mixed in a 3:2 ratio with the MORPHEUS crystallization screen condition E4 (Tube 2-4; 0.12 M Ethylene glycols 0.1 M Buffer System 1 pH 6.5 37.5 % v/v Precipitant Mix 4)
Crystal Properties Matthews coefficient Solvent content 1.98 37.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.03 α = 90 b = 64.571 β = 90 c = 73.536 γ = 90
Symmetry Space Group P 21 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 EIGER X 16M 2020-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979329 NSLS-II 17-ID-2
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 1.95 36.77 99.3 0.123 0.133 0.05 0.934 8.5 7.4 13064
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 1.95 1.99 95.1 0.783 0.838 0.291 0.893 7.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2CME 1.95 36.77 12363 639 99.5 0.2194 0.2175 0.2567 0.2536 RANDOM 33.585
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] -0.11 2.13 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.83 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 16.957 r_dihedral_angle_1_deg 8.277 r_angle_refined_deg 1.704 r_chiral_restr 0.105 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1249 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing