7SS5
Activated SgrAI endonuclease DNA-bound dimer with Ca2+ and intact primary site DNA
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6OBJ |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.974 |
f_angle_d | 0.54 |
f_chiral_restr | 0.04 |
f_plane_restr | 0.004 |
f_bond_d | 0.003 |
Sample |
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Activated filamentous SgrAI endonuclease with Ca2+ and intact primary site DNA |
Specimen Preparation | |
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Sample Aggregation State | FILAMENT |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C |
3D Reconstruction | |
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Reconstruction Method | HELICAL |
Number of Particles | 220067 |
Reported Resolution (Å) | 2.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | HELICAL |
Axial Symmetry | C1 |
Axial Rise | 21.2 |
Angular Rotation | -85.8 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (6OBJ) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Correlation coefficient | ||||
Overall B Value | 107.7 | ||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 55 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 2000 |
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 | 60240 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
IMAGE ACQUISITION | Leginon | |
CTF CORRECTION | Warp | |
MODEL FITTING | Coot | |
INITIAL EULER ASSIGNMENT | cryoSPARC | |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION |