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T.thermophilus 30S ribosome with KsgA, class K1k2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B3R
Sample 30S ribosomal with bound KsgA, a RNA methyltransferase at position 2 Sample Components 30S ribosomal subunit RNA methyltransferase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details After application of the complex, 15 seconds wait time was given before blotting.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 53393 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4B3R) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Overall B Value 80.1 Fitting Procedure Details Phenix was used in real space for initial refinement. The final refinements was performed with REFMAC within ccpem
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 43
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1800 Maximum Defocus (nm) 3500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 59000 Calibrated Magnification 101449 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Gautomatch IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 CTF CORRECTION RELION 3.1 MODEL FITTING Coot 0.9.5 MODEL FITTING UCSF Chimera 1.15 MODEL REFINEMENT PHENIX 1.19.2-4158 MODEL REFINEMENT REFMAC 5.8.0267 CLASSIFICATION 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