5MPS
Structure of a spliceosome remodeled for exon ligation
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.32 |
r_long_range_B_refined | 19.018 |
r_long_range_B_other | 19.018 |
r_dihedral_angle_3_deg | 14.397 |
r_dihedral_angle_4_deg | 14.129 |
r_dihedral_angle_1_deg | 9.753 |
r_scangle_other | 9.749 |
r_mcangle_it | 9.58 |
r_mcangle_other | 9.58 |
r_mcbond_it | 5.467 |
Sample |
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Saccharomyces cerevisiae spliceosome. Complex C just after Prp16-mediated remodeling |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK III |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3.5 microlitres sample were applied to the grid, left for 25 seconds and then blotted for 3.0-3.5 seconds before plunging. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 65824 |
Reported Resolution (Å) | 3.85 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Fourier Shell Correlation | ||||
Overall B Value | 330 | ||||
Fitting Procedure | |||||
Details | Used secondary structure restraints generated in ProSMART and LibG. |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 2 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 500 |
Maximum Defocus (nm) | 4500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 81000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | GIF Quantum energy filter, 20 eV slit width |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | RELION | 1.4 |
CTF CORRECTION | CTFFIND | 4 |
MODEL FITTING | Coot | 0.8.3 |
INITIAL EULER ASSIGNMENT | RELION | 1.4 |
FINAL EULER ASSIGNMENT | RELION | 1.4 |
CLASSIFICATION | RELION | 1.4 |
RECONSTRUCTION | RELION | 1.4 |
MODEL REFINEMENT | REFMAC | 5.8 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 350000 | Selected initial particles automatically using C complex 2D class averages, low-pass filtered to 20 Angstrom for automatic particle picking. |