5VRF
CryoEM Structure of the Zinc Transporter YiiP from helical crystals
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 3.765 |
| f_angle_d | 1.274 |
| f_chiral_restr | 0.056 |
| f_bond_d | 0.011 |
| f_plane_restr | 0.008 |
| Sample |
|---|
| YiiP dimer in an inward-facing conformation |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 72333 |
| Reported Resolution (Å) | 4.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Reconstruction was achieved using the IHRSR method implemented in RELION 2.0. |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | D5 |
| Axial Rise | 28.2 |
| Angular Rotation | -17 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3J1Z, 3J1Z) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | The residues were manually adjusted in COOT relying on the large side-chain residues, and the whole system was further optimized using the real_space_ ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 70 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 2500 |
| 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 | 22500 |
| Calibrated Magnification | |
| Source | LAB6 |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | SPARX/EMAN2 | EMAN2.1 |
| PARTICLE SELECTION | RELION | 2.0 |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | CTFFIND | 4.1 |
| CTF CORRECTION | Gctf | 0.50 |
| MODEL FITTING | Coot | 0.8.6 |
| INITIAL EULER ASSIGNMENT | RELION | 2.0 |
| FINAL EULER ASSIGNMENT | RELION | 2.0 |
| CLASSIFICATION | RELION | 2.0 |
| RECONSTRUCTION | RELION | 2.0 |
| MODEL REFINEMENT | PHENIX | 1.11 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 141904 | 2293 filaments selected with SPARX/EMAN2, then windowed into 141,904 segments (450x450 pixel overlapping segments) | ||
