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Cryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Sample RC-dLH complex model II from Gemmatimonas groenlandica
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details blot time, 3 sec
blot force, 3
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 116858 Reported Resolution (Å) 2.3 Resolution Method FSC 0.143 CUT-OFF Other Details performed in cryosparc Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target map to model Overall B Value 60 Fitting Procedure Details Initial model was established with coot. The model was fitted into map using chimera. The refinement was performed y the use of Phenix.
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.2.1 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.0 MODEL FITTING Coot 0.8.9.2 INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 CLASSIFICATION cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1 MODEL REFINEMENT PHENIX 1.20.1-4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF collection was performed within cryosparc 935540 cryosparc blob selection first, then model reference selection for final 3d reconstruction