7NXD
Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 16.557 |
| f_angle_d | 1.48 |
| f_chiral_restr | 0.194 |
| f_plane_restr | 0.029 |
| f_bond_d | 0.013 |
| Sample |
|---|
| Dimeric complex of integrin a5b1 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 98750 |
| Reported Resolution (Å) | 4.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4WK0, 4WK0, 3VI3, 3VI3, 3FCS, 3FCS) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | GATAN K3 BIOQUANTUM (6k x 4k) | |||||||
| Electron Dose (electrons/Å**2) | 65.8 | 82.3 | |||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | -500 |
| Maximum Defocus (nm) | 3200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.62 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | |
| FINAL EULER ASSIGNMENT | RELION | 3.0 |
| CLASSIFICATION | RELION | 3.0 |
| RECONSTRUCTION | RELION | 3.0 |
| MODEL REFINEMENT | Coot | |
| MODEL REFINEMENT | PHENIX | 1.17.1 Release 3660 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 496356 | 1424 particles were manually picked and used to obtain 2D classes with distinct features as templates for Gautomatch | ||
