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Granulovirus occlusion bodies by serial electron diffraction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0Z
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.2 α = 90 b = 103.2 β = 90 c = 103.2 γ = 90
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY FREE R-VALUE 1.6 1.6 1.33 26635 1297 99.95 0.1718 0.1705 0.1965 19.29
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 6.1208 f_angle_d 1.1313 f_chiral_restr 0.0767 f_bond_d 0.0116 f_plane_restr 0.0072
Software Software Software Name Purpose phenix.refine refinement PHENIX refinement
Sample Cydia pomonella granulosis virus (isolate Mexican)
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 1.6 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 103.2 Length b 103.2 Length c 103.2 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (5G0Z) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type OTHER Electron Dose (electrons/Å**2) 4.7
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI F20 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version MODEL FITTING Coot 0.8.9.2 MOLECULAR REPLACEMENT PHENIX 1.17 RECONSTRUCTION Coot MODEL REFINEMENT PHENIX 1.17
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE Data reduction and structure solution using X-ray crystallography codes (CrystFEL, Phaser, cctbx.xfel, Coot)