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KimA from B. subtilis with nucleotide second-messenger c-di-AMP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S3K
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.668 f_angle_d 0.72 f_chiral_restr 0.044 f_bond_d 0.006 f_plane_restr 0.005
Sample KimA with bound c-di-AMP
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 332000 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (6S3K) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 55
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1100 Maximum Defocus (nm) 2500 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) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION Gctf MODEL FITTING Coot MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION