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CryoEM structure of the apo-SrpI encapasulin complex from Synechococcus elongatus PCC 7942
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.865 f_angle_d 0.663 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.006
Sample SrpI encapsulin apo complex
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot force 5, 3 sec blot, 100 humidity, 4C, 1 sec drain time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 34425 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value 20 Fitting Procedure Details One subunit was built completely de novo based on sequence/density, and iteratively real space refined with neighboring subunits using PHENIX.
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI ARCTICA Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.6 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 36000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details Residual beam tilt corrected in RELION/3.1. CTF refinement performed in RELION/3.1.
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.1.10 MODEL FITTING PHENIX 1.18_3845 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.18_3845
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF refinement was performed in Relion/3.1 57431 Relion LoG autopicker to select particles