7NTM
Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.569 |
r_dihedral_angle_4_deg | 20.792 |
r_dihedral_angle_3_deg | 18.792 |
r_dihedral_angle_1_deg | 9.091 |
r_scbond_it | 8.936 |
r_long_range_B_refined | 8.795 |
r_mcbond_it | 7.134 |
r_angle_refined_deg | 6.76 |
r_mcangle_it | 6.571 |
r_chiral_restr | 0.582 |
Sample |
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Tetrameric structure of native ADH1 from S. cereviciae in its apo state. |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 222802 |
Reported Resolution (Å) | 2.86 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | D2 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (5ENV) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | BACKBONE TRACE | ||||
Refinement Target | |||||
Overall B Value | 123 | ||||
Fitting Procedure | |||||
Details | Model building and refinement were done using using CCP-EM software suite (Burnley et al, 2017). The X-ray structure of yeast ADH1 (PDB: 5ENV) was us ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 60 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 3000 |
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 | 130000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | Warp | 40 |
IMAGE ACQUISITION | EPU | 2.7 |
CTF CORRECTION | Warp | 40 |
MODEL FITTING | MOLREP | |
INITIAL EULER ASSIGNMENT | cryoSPARC | v2.15.041 |
FINAL EULER ASSIGNMENT | cryoSPARC | v2.15.041 |
RECONSTRUCTION | cryoSPARC | v2.15.041 |
MOLECULAR REPLACEMENT | MOLREP | |
MODEL REFINEMENT | REFMAC | 5 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 639189 |