7W8J
Dimethylformamidase, 2x(A2B2)
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6LVB | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.441 |
| r_dihedral_angle_3_deg | 13.68 |
| r_dihedral_angle_4_deg | 11.908 |
| r_dihedral_angle_1_deg | 5.515 |
| r_angle_refined_deg | 1.236 |
| r_angle_other_deg | 1.107 |
| r_long_range_B_refined | 0.279 |
| r_long_range_B_other | 0.278 |
| r_chiral_restr | 0.044 |
| r_bond_other_d | 0.031 |
| Sample |
|---|
| DMFase, an amidohydrolase |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | wait time - 10 seconds and 3.5 seconds blot |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 28964 |
| Reported Resolution (Å) | 2.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | The final reconstruction was from a single 3D class after B-factor weighting and aberration correction in Relion 3.1 |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6LVB, 6LVB) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | 73.98 | ||||
| Fitting Procedure | |||||
| Details | Servalcat was used along with Refmac to calculate fofc maps and extensively used for modelling. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 28.3 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 850 |
| Maximum Defocus (nm) | 3200 |
| 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 | 75000 |
| Calibrated Magnification | 130841 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Gautomatch | |
| IMAGE ACQUISITION | EPU | 1.10 |
| CTF CORRECTION | Gctf | 1.06 |
| MODEL FITTING | Coot | 0.9.5 |
| MODEL FITTING | UCSF Chimera | 1.15 |
| MODEL REFINEMENT | REFMAC | 5.8.0267 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | RELION | 3.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 114182 | |||
