Cryo-EM structure of H. neapolitanus CsoSCA in reducing conditions, dimer, minor state
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_dihedral_angle_6_deg | 14.8087 |
| s_dihedral_angle_3_deg | 13.0192 |
| s_dihedral_angle_1_deg | 7.0739 |
| s_dihedral_angle_2_deg | 3.9044 |
| s_angle_nonh_deg | 2.0034 |
| s_nbtor | 0.2388 |
| s_hbond_nbd | 0.2328 |
| s_nbd | 0.2283 |
| s_metal_ion | 0.1319 |
| s_chiral_restr | 0.0861 |
| Sample |
|---|
| HnCsoSCA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 4C, 100% relative humidity, delay time 0s, blot time 3s, blot force 0 |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 200733 |
| Reported Resolution (Å) | 2.27 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 64.757 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 600 |
| Maximum Defocus (nm) | 1800 |
| 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 | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | 0.2.5 |
| IMAGE ACQUISITION | EPU | 3.6.0 |
| CTF CORRECTION | cryoSPARC | 4.7 |
| MODEL FITTING | UCSF ChimeraX | 1.9 |
| MODEL FITTING | ISOLDE | 1.9 |
| MODEL REFINEMENT | Servalcat | 0.4.99 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.7 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.7 |
| CLASSIFICATION | cryoSPARC | 4.7 |
| RECONSTRUCTION | cryoSPARC | 4.7 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 818243 | Particles were picked with topaz, trained with a set of about 1000 particles picked manually from micrographs denoised by CryoSPARC. Topaz was trained and applied on raw micrographs. | ||
