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Crystal structure and proteomics analysis of empty virus like particles of Cowpea mosaic virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NY7 PDB ENTRY 1NY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 0.1M SODIUM ACETATE PH 4.7 3-4%(W/V)PEG 3350 0.3M AMMONIUM SULFATE 5% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.95 68.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 655.97 α = 90 b = 655.97 β = 90 c = 571.451 γ = 90
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 6M MIRRORS 2015-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 2.3 50 60.3 0.29 3.7 2.3 3192363 1.7 1.48
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 2.3 2.42 49.6 0.45 1.7 1.8
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NY7 2.3 10 3 3192363 95172 58.3 0.359 0.359 0.362 RANDOM 24.75
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 x_dihedral_angle_d 29.378 x_angle_deg 1.566 x_improper_angle_d 0.77 x_bond_d 0.011 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 29.378 x_angle_deg 1.566 x_improper_angle_d 0.77 x_bond_d 0.011 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4382 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose X-PLOR refinement HKL-2000 data reduction SCALEPACK data scaling SCALA data scaling PHASER phasing