6VJA
Structure of CD20 in complex with rituximab Fab
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 16.01 |
| f_angle_d | 1.215 |
| f_chiral_restr | 0.064 |
| f_bond_d | 0.013 |
| f_plane_restr | 0.006 |
| Sample |
|---|
| CD20 in complex with rituximab Fab |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 5s blot time |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 149322 |
| Reported Resolution (Å) | 3.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | No data beyond 1/5 A-1 were used in refinement |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (2OSL) | 2 | |||
| Refinement Space | REAL | REAL | |||
| Refinement Protocol | AB INITIO MODEL | FLEXIBLE FIT | |||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Atomic model for CD20 was built ab initio and manually in COOT. It was then re-built using ISOLDE, and finally refined in Phenix. | The X-ray crystallographic atomic model for Rituximab Fab was rigid-body fit into the map, modified using Cootand ISOLDE, and refined with Phenix | |||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 53 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| 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 | 165000 |
| Calibrated Magnification | 58906 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cisTEM | |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | cisTEM | |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | cisTEM | |
| FINAL EULER ASSIGNMENT | cisTEM | |
| CLASSIFICATION | cisTEM | |
| RECONSTRUCTION | cisTEM | |
| MODEL REFINEMENT | PHENIX | |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | |
| MODEL FITTING | ISOLDE | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 4114800 | 15,630 movies were selected because of the quality of their CTF fits. 4,114,800 coordinates were selected, leading to 466,632 particles which clustered into high-quality 2D class averages | ||
