8TKQ
Cryo-EM structure of human full-length RAD52
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KN0 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 2.58 |
f_angle_d | 0.574 |
f_chiral_restr | 0.044 |
f_bond_d | 0.007 |
f_plane_restr | 0.003 |
Sample |
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Human RAD52 undecameric structure |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 623559 |
Reported Resolution (Å) | 2.5 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C11 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1KN0) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | 130.2 | ||||
Fitting Procedure | |||||
Details | Initial fitting was done in Chimera followed by refinement with Namdinator and then PHENIX alone |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 50 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 2200 |
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 | No tilt data and tilted data (30 deg) was collected at the same time and processed together |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 3.3.2 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | cryoSPARC | 3.3.2 |
MODEL FITTING | Coot | |
INITIAL EULER ASSIGNMENT | cryoSPARC | |
FINAL EULER ASSIGNMENT | cryoSPARC | |
RECONSTRUCTION | cryoSPARC | 3.3.2 |
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 | 2261059 | Template based picking from no tilt and 30 deg tilt data to deal with preferred orientation |