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TolQ inner membrane protein from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 32.442 r_long_range_B_other 32.442 r_scangle_other 23.109 r_dihedral_angle_2_deg 21.889 r_mcangle_it 16.895 r_mcangle_other 16.888 r_dihedral_angle_3_deg 16.506 r_scbond_it 13.603 r_scbond_other 13.595 r_mcbond_it 11.053
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 32.442 r_long_range_B_other 32.442 r_scangle_other 23.109 r_dihedral_angle_2_deg 21.889 r_mcangle_it 16.895 r_mcangle_other 16.888 r_dihedral_angle_3_deg 16.506 r_scbond_it 13.603 r_scbond_other 13.595 r_mcbond_it 11.053 r_mcbond_other 11.044 r_dihedral_angle_4_deg 9.465 r_dihedral_angle_1_deg 6.46 r_angle_refined_deg 1.447 r_angle_other_deg 1.333 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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 TolQ inner membrane protein
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 215170 Reported Resolution (Å) 3.02 Resolution Method FSC 0.143 CUT-OFF Other Details Map was post processed using DeepEMHancer to guide refinement. The deposited maps are pre-DeepEMHancer Refinement Type Symmetry Type POINT Point Symmetry C5
Map-Model Fitting and Refinement Id 1 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) 100
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch motion and patch CTF correction with binning to 0.833 A/pixel. 472724 Manual picking to generate templates. Template based autopicking to get 472724 particles. Iterative 2D classification to get 246741 particles.