☰ Navigation Tabs
cryo-EM structure of AccA3/AccD4/AccD5/AccE5 complex from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.018 r_lrange_other 17.018 r_dihedral_angle_6_deg 15.931 r_dihedral_angle_3_deg 11.946 r_scangle_it 11.748 r_scangle_other 11.748 r_mcangle_it 8.525 r_mcangle_other 8.525 r_scbond_it 7.348 r_scbond_other 7.348
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.018 r_lrange_other 17.018 r_dihedral_angle_6_deg 15.931 r_dihedral_angle_3_deg 11.946 r_scangle_it 11.748 r_scangle_other 11.748 r_mcangle_it 8.525 r_mcangle_other 8.525 r_scbond_it 7.348 r_scbond_other 7.348 r_dihedral_angle_1_deg 6.886 r_dihedral_angle_2_deg 6.264 r_mcbond_it 5.69 r_mcbond_other 5.69 r_angle_refined_deg 1.907 r_angle_other_deg 0.631 r_ncsr_local_group_7 0.292 r_ncsr_local_group_5 0.235 r_ncsr_local_group_4 0.232 r_ncsr_local_group_3 0.227 r_ncsr_local_group_2 0.225 r_ncsr_local_group_1 0.223 r_ncsr_local_group_6 0.22 r_nbd_refined 0.179 r_symmetry_nbd_other 0.177 r_ncsr_local_group_15 0.156 r_nbtor_refined 0.149 r_ncsr_local_group_8 0.128 r_ncsr_local_group_10 0.112 r_ncsr_local_group_14 0.11 r_ncsr_local_group_9 0.107 r_ncsr_local_group_13 0.105 r_ncsr_local_group_11 0.101 r_ncsr_local_group_12 0.094 r_chiral_restr 0.088 r_xyhbond_nbd_refined 0.08 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d
Sample AccA3/AccD4/AccD5/AccE5 complex from Mycobacterium smegmatis
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 251974 Reported Resolution (Å) 2.35 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 44.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2250 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING UCSF ChimeraX 1.10.1 MODEL REFINEMENT Servalcat INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1279569