8U8V
Cryo-EM structure of Substrate ATP Bound in the Insertion Site (IS) of Human Mitochondrial Transcription Elongation Complex
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5OLA |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.1 |
f_angle_d | 0.697 |
f_chiral_restr | 0.044 |
f_plane_restr | 0.006 |
f_bond_d | 0.004 |
Sample |
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Substrate ATP Bound to Insertion Site (IS) of Human Mitochondrial Transcription Elongation Complex |
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 | 331858 |
Reported Resolution (Å) | 2.74 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Non-uniform Refinement (CryoSPARC) which is an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps durin ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (5OLA) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Cross-correlation Coefficient | ||||
Overall B Value | 45 | ||||
Fitting Procedure | |||||
Details | Initial Fitting was done in Chimera and flexible/refined fitting done with Coot Phenix Real-Space Refinement. |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 (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) | 500 |
Maximum Defocus (nm) | 1800 |
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 | 105000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Preliminary grid screening performed manually using TFS Glacios. |
EM Software | ||
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Task | Software Package | Version |
MODEL REFINEMENT | PHENIX | 1.21rc1_5015: |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 4798227 | Automated particle picking (Blob picker, CryoSPARC) with manual inspection (Inspect Particle Picks). |