5GAO
Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4BGD |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 49.736 |
r_long_range_B_other | 49.735 |
r_scangle_other | 36.329 |
r_dihedral_angle_2_deg | 35.002 |
r_mcangle_it | 33.984 |
r_mcangle_other | 33.983 |
r_scbond_it | 21.114 |
r_mcbond_it | 21.107 |
r_mcbond_other | 21.099 |
r_scbond_other | 21.098 |
Sample |
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Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 140155 |
Reported Resolution (Å) | 4.2 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
---|---|---|---|---|---|
Id | 1 (4BGD, 4BGD) | ||||
Refinement Space | RECIPROCAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 38 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 500 |
Maximum Defocus (nm) | 3500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 81000 |
Calibrated Magnification | 35714 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | RELION | |
IMAGE ACQUISITION | DigitalMicrograph | |
CTF CORRECTION | CTFFIND | 4 |
MODEL FITTING | Coot | 0.8.3 |
MODEL REFINEMENT | REFMAC | 5.8 |
INITIAL EULER ASSIGNMENT | RELION | |
FINAL EULER ASSIGNMENT | RELION | |
CLASSIFICATION | RELION | |
RECONSTRUCTION | RELION |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING ONLY | 473827 |