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CryoEM structure of human MICAL1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BRY experimental model PDB 4TXI experimental model PDB 5LE0
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.4847 f_angle_d 0.4841 f_chiral_restr 0.0382 f_plane_restr 0.0036 f_bond_d 0.003
Sample MICAL1 with the FAD cofactor
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 84863 Reported Resolution (Å) 3.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (2BRY, 4TXI, 5LE0) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 77.02 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 21
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1400 Maximum Defocus (nm) 2800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification 59981 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.1 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING UCSF ChimeraX 1.3 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION RELION 4.0 MODEL REFINEMENT PHENIX 1.21-5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 6256757