7XOJ
Cryo-EM structure of GroEL bound to unfolded substrate (UGT1A) at 2.8 Ang. resolution (Consensus Refinement)
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 3.552 |
| f_angle_d | 0.461 |
| f_chiral_restr | 0.039 |
| f_bond_d | 0.003 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| GroEL-UGT1A complex |
| Sample Components |
| GroEL |
| UDP-glucuronosyltransferase 1A (UGT1A) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3 ul of 33 mg/ml GroEL-UGT1A was placed on Holey carbon Quanitifoil copper grids (300 mesh size R1.2/1.3) and blotted for 3 seconds (blot force =1) |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 1202095 |
| Reported Resolution (Å) | 2.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | 91 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 2000 |
| 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 | 3.1 |
| IMAGE ACQUISITION | EPU | |
| IMAGE ACQUISITION | RELION | 3.1 |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | UCSF ChimeraX | 1.2.5 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| RECONSTRUCTION | RELION | 3.1 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | Using RELIONs own implementation of CTFFIND4.1 --Box 512 --ResMin 30 --ResMax 2 --dFMin 5000 --dFMax 50000 --FStep 250 --dAst 100 | 1289236 | Parameters for auto picking (LoG) single particles from motion-corrected micrographs with estimated CTF parameters resulted in 1,289,236 particles picked (average of 437 particles per micrograph). All particle images were then extracted with a box size of 300 pixels and a spherical mask diameter of 240 A for 2D classification. | |
