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Structure of VcINDY-alpha ketoglutarate complex in Ci-Ci conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7T9F
Sample Dimer of VcINDY in complex with alpha ketoglutarate
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 290548 Reported Resolution (Å) 2.35 Resolution Method FSC 0.143 CUT-OFF Other Details C2 Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7T9F) Refinement Space REAL Refinement Protocol OTHER Refinement Target cross-correlation coefficient Overall B Value 52.28 Fitting Procedure Details Initial local fitting was done using Chimera and then coot was used for ajustment.
Data Acquisition Detector Type GATAN K3 BIOCONTINUUM (6k x 4k) Electron Dose (electrons/Å**2) 53.11
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 1600 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 105000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp 1.0.9 PARTICLE SELECTION Topaz 0.2.5a IMAGE ACQUISITION Leginon 3.5 CTF CORRECTION cryoSPARC v 4.4.1 MODEL FITTING UCSF Chimera 1.15 MODEL FITTING Coot 0.9.6 MODEL REFINEMENT PHENIX 1.20.1_4487 INITIAL EULER ASSIGNMENT cryoSPARC v 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC v 4.4.1 CLASSIFICATION cryoSPARC v 4.4.1 RECONSTRUCTION cryoSPARC V 4.4.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3717199 Particles were selected from 3948 untilted images