6TG9
Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.254 |
f_angle_d | 0.775 |
f_chiral_restr | 0.056 |
f_bond_d | 0.01 |
f_plane_restr | 0.003 |
Sample |
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Formate dehydrogenase, NADH reduced |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 199229 |
Reported Resolution (Å) | 3.24 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (1FDO, 3IAM, 5XF9) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | BACKBONE TRACE | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | GATAN K2 SUMMIT (4k x 4k) | GATAN K2 SUMMIT (4k x 4k) | |||||||
Electron Dose (electrons/Å**2) | 64 | 40 |
Imaging Experiment | 1 | 2 |
---|---|---|
Date of Experiment | ||
Temperature (Kelvin) | ||
Microscope Model | FEI POLARA 300 | FEI TITAN KRIOS |
Minimum Defocus (nm) | ||
Maximum Defocus (nm) | ||
Minimum Tilt Angle (degrees) | ||
Maximum Tilt Angle (degrees) | ||
Nominal CS | ||
Imaging Mode | BRIGHT FIELD | BRIGHT FIELD |
Specimen Holder Model | ||
Nominal Magnification | ||
Calibrated Magnification | ||
Source | FIELD EMISSION GUN | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
CTF CORRECTION | CTFFIND | 4.1.10 |
MODEL FITTING | Coot | 0.8 |
INITIAL EULER ASSIGNMENT | IMAGIC | |
FINAL EULER ASSIGNMENT | RELION | 3.0 |
RECONSTRUCTION | RELION | 3.0 |
MODEL REFINEMENT | PHENIX | 1.14 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | CTFFIND4 was used to estimate contrast transfer function parameters. CTF correction was done in Relion 3.0. |