8PTY
Cryo-EM structure of human Elp123 in complex with 5'-deoxyadenosine and methionine
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 4.68 |
f_angle_d | 0.597 |
f_chiral_restr | 0.045 |
f_bond_d | 0.004 |
f_plane_restr | 0.004 |
Sample |
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Human Elp123 in complex with 5'-deoxyadenosine and methionine |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | 15 s wait time, blot force 5, 5 s blot time |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 171951 |
Reported Resolution (Å) | 3.58 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | |||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS KRIOS |
Minimum Defocus (nm) | 900 |
Maximum Defocus (nm) | 2700 |
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 | 96000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | |
PARTICLE SELECTION | Topaz | |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | cryoSPARC | |
MODEL FITTING | UCSF ChimeraX | |
MODEL FITTING | NAMD | |
INITIAL EULER ASSIGNMENT | cryoSPARC | |
FINAL EULER ASSIGNMENT | RELION | |
CLASSIFICATION | RELION | |
RECONSTRUCTION | RELION | |
MODEL REFINEMENT | Coot | |
MODEL REFINEMENT | PHENIX |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 264351 | given number of particles from TOPAZ picking, and after 3D curation |