6T2V
Cryo-EM structure of the RecBCD in complex with Chi-plus2 substrate
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5LD2 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.6839 |
f_angle_d | 0.3966 |
f_chiral_restr | 0.0343 |
f_plane_restr | 0.0052 |
f_bond_d | 0.0014 |
Sample |
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RecBCD bound to a forked DNA substrate that contain Chi-plus2 |
Sample Components |
RecBdCD |
Chi-plus2 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 1s blot before plunging |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 380912 |
Reported Resolution (Å) | 3.8 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (5LD2) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Rounds of manual structure editing in coot and real-space refinement with Phenix |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 75.9 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1200 |
Maximum Defocus (nm) | 2700 |
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 | |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | Gautomatch | |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | Gctf | |
INITIAL EULER ASSIGNMENT | RELION | 3 |
FINAL EULER ASSIGNMENT | RELION | 3 |
CLASSIFICATION | RELION | 3 |
RECONSTRUCTION | RELION | 3 |
MODEL REFINEMENT | PHENIX | 1.12 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 754150 |