8EAJ
SsoMCM hexamer bound to Mg/ADP-BeFx and 46-mer DNA strand. Class 1
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6MII |
Sample |
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SsoMCM hexamer bound to Mg/ADP-BeFx and 46-mer DNA strand. Class 1. |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 832313 |
Reported Resolution (Å) | 2.45 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (6MII) | ||||
Refinement Space | |||||
Refinement Protocol | OTHER | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Bond distance and angle restraints for a tetrahedral Zn2+ coordination were applied. Bond distance and angle restraints for a octahedral Mg2+ coordina ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 78 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 1800 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 2.14.2 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | cryoSPARC | 2.14.2 |
MODEL FITTING | PHENIX | 1.20.1_4487 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 2.14.2 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.31 |
CLASSIFICATION | cryoSPARC | 3.31 |
RECONSTRUCTION | cryoSPARC | 3.31 |
MODEL REFINEMENT | PHENIX | 1.20.1_4487 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Initial CTF was calculated by cryoSPARC Patch CTF. CTF parameters were refined during final homogeneous refinement in cryoSPARC. | Particles were selected from a subset of micrographs with cryoSPARC blob picker. 2D class averages were calculated, selected and used as templates with cryoSPARC template picker. |