8A64
cryoEM structure of the catalytically inactive EndoS from S. pyogenes in complex with the Fc region of immunoglobulin G1.
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 5.917 |
| f_angle_d | 0.848 |
| f_chiral_restr | 0.056 |
| f_bond_d | 0.008 |
| f_plane_restr | 0.006 |
| Sample |
|---|
| Complex of the EndoS from S. pyogenes and the Fc region of Immunoglobulin G |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK II |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | single blot |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 339309 |
| Reported Resolution (Å) | 4.6 |
| Resolution Method | FSC 3 SIGMA CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6EN3, 1H3X, 1H3X) | ||||
| Refinement Space | |||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Initial PDB models were rigid-body refined for individual chains. Later, the model was real-space refined removing side chains that couldn't be assign ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 59.4 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1300 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | RELION | |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | PHENIX | |
| INITIAL EULER ASSIGNMENT | RELION | |
| FINAL EULER ASSIGNMENT | cryoSPARC | |
| CLASSIFICATION | cryoSPARC | |
| RECONSTRUCTION | cryoSPARC | |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | RELION CTFfind4 implementation | 797351 | ||
