5VRF
CryoEM Structure of the Zinc Transporter YiiP from helical crystals
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3J1Z |
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) |