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Structure of human SIT1 bound to L-pipecolate (focussed map / refinement)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M18
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.122 f_angle_d 0.545 f_chiral_restr 0.04 f_plane_restr 0.006 f_bond_d 0.003
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details grid blotted for 4sec after a 20sec wait time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 344606 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details cryoSPARC masked local refinement focussed on SIT1 with symmetry expanded particles after 3D classification in RELION Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6M18) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value 112 Fitting Procedure Details Initial model fitting was peformed in Chimera and model building in COOT
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2400 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING Coot 0.9.6 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION RELION 3.1.3 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX 1.20_4459
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 808912 particles from template and TOPAZ trained picking after initial 2D classification to remove junk