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Virus-like particle of Beihai levi-like virus 21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% PEG 400, 0.2 M sodium citrate, 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 5.91 79.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 296.937 α = 90 b = 306.875 β = 90 c = 322.559 γ = 90
Symmetry Space Group I 2 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 2018-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.089 48.938 99.1 0.358 0.395 0.985 5.56 5.665 264708 66.517
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.09 3.28 95.4 2.785 3.074 0.221 0.58 5.542
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 THROUGHOUT 2ms2 3.089 48.938 1.33 263402 9929 98.72 0.2663 0.2661 0.2675 0.271 0.2741 80.8487
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 43650 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction FFT phasing