☰ Navigation Tabs
Cryo-EM structure of CdaA-DAC domain in complex with GlmM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.44 f_angle_d 0.499 f_chiral_restr 0.046 f_bond_d 0.002 f_plane_restr 0.002
Sample Diadenylate cyclase CdaA, Phosphoglucosamine mutase GlmM,
ATP
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details 13.2 uM of GlmM and 10 mM of Mn-ATP were added prior to sample application onto the grids. Grids were blotted for 4 seconds.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 133430 Reported Resolution (Å) 4.84 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 53.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 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 49407 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.8.4 IMAGE ACQUISITION SerialEM ver4.0.6 CTF CORRECTION CTFFIND 4.1.13 MODEL FITTING Coot 0.9.8.91 INITIAL EULER ASSIGNMENT RELION 5.0-beta FINAL EULER ASSIGNMENT RELION 5.0-beta RECONSTRUCTION RELION 5.0-beta MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1908105