5NP7
CryoEM structure of Human Rad51 on single-stranded DNA to 4.2A resolution.
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 44.967 |
| r_dihedral_angle_2_deg | 37.024 |
| r_dihedral_angle_3_deg | 23.006 |
| r_mcangle_it | 19.492 |
| r_dihedral_angle_4_deg | 18.909 |
| r_scbond_it | 15.798 |
| r_mcbond_it | 11.5 |
| r_dihedral_angle_1_deg | 6.724 |
| r_angle_refined_deg | 2.647 |
| r_chiral_restr | 0.21 |
| Sample |
|---|
| Helical filament of HRAD51 on single-stranded DNA with AMPPNP |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | |
| Cryogen Name | NITROGEN |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 60000 |
| Reported Resolution (Å) | 4.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Helical segments were divided in half, not drawn randomly or odd/even as this would result in some segments from the same filament in both half models ... |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 16 |
| Angular Rotation | 56.2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Maximum likelihood | ||||
| Overall B Value | 94.574 | ||||
| Fitting Procedure | |||||
| Details | Backbone fitting is good but many of the sidechains cannot be relied on as the map resolution was insufficient. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 20 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 2000 |
| Maximum Defocus (nm) | |
| 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 | 59000 |
| Calibrated Magnification | 104477 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Ximdisp | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | Coot | |
| CLASSIFICATION | RELION | 1.4 |
| RECONSTRUCTION | RELION | 1.4 |
| MODEL REFINEMENT | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | per segment | 70000 | ||
