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Structure of the HCV IRES binding to the 40S ribosomal subunit, closed conformation. Structure 1(delta dII)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D9J experimental model PDB 5FLX experimental model PDB 5K0Y experimental model PDB 4UJD
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.294 f_angle_d 0.737 f_chiral_restr 0.039 f_plane_restr 0.006 f_bond_d 0.003
Sample 40S ribosomal small subunit with HCV IRES
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details 4 second blot time, force 3
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 42271 Reported Resolution (Å) 4.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6D9J, 5FLX, 5K0Y, 4UJD) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 70.9
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI F30 Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.26 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 52000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Leginon CTF CORRECTION CTFFIND MODEL FITTING UCSF Chimera 1.15 MODEL FITTING Coot 0.9.3 MODEL REFINEMENT PHENIX 1.19.1-4122 INITIAL EULER ASSIGNMENT RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION