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Cryo-EM structure of the Lysenin Pore
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZXD
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.002 r_long_range_B_refined 25.055 r_long_range_B_other 25.055 r_scangle_other 19.592 r_mcangle_it 13.252 r_mcangle_other 13.252 r_scbond_it 11.681 r_scbond_other 11.68 r_dihedral_angle_3_deg 11.634 r_mcbond_it 9.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.002 r_long_range_B_refined 25.055 r_long_range_B_other 25.055 r_scangle_other 19.592 r_mcangle_it 13.252 r_mcangle_other 13.252 r_scbond_it 11.681 r_scbond_other 11.68 r_dihedral_angle_3_deg 11.634 r_mcbond_it 9.124 r_mcbond_other 9.124 r_dihedral_angle_4_deg 8.954 r_dihedral_angle_1_deg 5.564 r_angle_refined_deg 1.063 r_angle_other_deg 0.792 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample Membrane-inserted form of the nonameric pore forming protein Lysenin
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 29329 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C9
Map-Model Fitting and Refinement Id 1 (3ZXD) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details Initial docking of C-terminal region of lysenin monomer to EM map was performed using UCSF Chimera followed by model N-terminal extension in COOT.
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 47
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 4500 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 81000 Calibrated Magnification 34965 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Direct alignments: Beam tilt pivot points, Beam shift, Comma Free. C2 aperture centering, C2 lens astigmatism correction. Objective aperture centering and objective lens astigmatism correction. Energy filter Tuning and occasional ZLP centering.
EM Software Task Software Package Version PARTICLE SELECTION RELION 1.4 IMAGE ACQUISITION Titan User Interface CTF CORRECTION Gctf MODEL FITTING Coot 0.8.2 INITIAL EULER ASSIGNMENT RELION 1.4 FINAL EULER ASSIGNMENT RELION 1.4 CLASSIFICATION RELION 1.4 RECONSTRUCTION RELION 1.4 MODEL REFINEMENT REFMAC 5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 53779 Autopicking performed with RELION after manually picking 1000 particles to create 2D Classes (references) for autopicking.