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Single particle reconstruction of glucose isomerase from Streptomyces rubiginosus based on data acquired in the presence of substantial aberrations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VR0
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.248 r_dihedral_angle_4_deg 16.595 r_long_range_B_refined 16.001 r_dihedral_angle_3_deg 13.633 r_mcangle_it 8.608 r_scbond_it 7.081 r_mcbond_it 5.417 r_dihedral_angle_1_deg 5.405 r_angle_refined_deg 1.602 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.248 r_dihedral_angle_4_deg 16.595 r_long_range_B_refined 16.001 r_dihedral_angle_3_deg 13.633 r_mcangle_it 8.608 r_scbond_it 7.081 r_mcbond_it 5.417 r_dihedral_angle_1_deg 5.405 r_angle_refined_deg 1.602 r_chiral_restr 0.115 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 61909 Reported Resolution (Å) 2.7 Resolution Method FSC 0.143 CUT-OFF Other Details We used the approach implemented in cisTEM. Refinement Type Symmetry Type POINT Point Symmetry D2
Map-Model Fitting and Refinement Id 1 (5VR0) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target REFMAC Overall B Value Fitting Procedure Details COOT was crucial as well.
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 120
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS TALOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details The goal of the experiment was to show that it is possible to perform high resolution reconstruction in the presence of higher order aberrations.
EM Software Task Software Package Version PARTICLE SELECTION cisTEM IMAGE ACQUISITION SerialEM CTF CORRECTION cisTEM MODEL FITTING MOLREP INITIAL EULER ASSIGNMENT cisTEM MODEL REFINEMENT REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 114522