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 | |
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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 |
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Complex of the EndoS from S. pyogenes and the Fc region of Immunoglobulin G |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK II |
Cryogen Name | ETHANE |
Sample Vitrification Details | single blot |
3D Reconstruction | |
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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 | |||||
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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 | |||||||||
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Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 59.4 |
Imaging Experiment | 1 |
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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 | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | RELION CTFfind4 implementation | 797351 |