☰ Navigation Tabs
Crystal structure of SARS-CoV-2 soluble dimeric ORF9b
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 291 2.0M ammonium phosphate monobasic, 0.1M Tris pH 8
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.579 α = 90 b = 73.579 β = 90 c = 175.616 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 315 2020-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.95 50 99.8 0.061 34.357 17.1 12167
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.06 100 0.671 4.569 16.2
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 2CME 2.95 31.15 1.36 12059 561 99.21 0.2691 0.2657 0.2692 0.2892 0.2977 43.99
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 21.0066 f_angle_d 0.7329 f_chiral_restr 0.0456 f_bond_d 0.0047 f_plane_restr 0.0037
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2306 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 17
Software Software Software Name Purpose PDB_EXTRACT data extraction PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing