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Virus-like particle of Beihai levi-like virus 19
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 8 293 66% MPD, 100 mM Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 6.49 81.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 298.111 α = 90 b = 325.048 β = 90 c = 346.016 γ = 90
Symmetry Space Group P 21 21 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 2017-09-01 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 3.79 49.431 98 0.372 0.44 0.965 3.55 3.41 323225 83.511
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 3.79 4.02 95.3 1.495 1.772 0.243 0.77 3.358
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 3.794 41.392 1.34 322856 9968 97.96 0.2611 0.2609 0.2628 0.2668 0.2683 107.1578
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 89040 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 30
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX refinement PDB_EXTRACT data extraction FFT phasing