4V4W
Structure of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143
ELECTRON MICROSCOPY
Sample |
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SecM-stalled E. coli ribosome complex |
Sample Components |
30S ribosomal protein S2 |
30S ribosomal subunit protein S3 |
30S ribosomal subunit protein S4 |
30S ribosomal subunit protein S5 |
30S ribosomal subunit protein S6 |
30S ribosomal subunit protein S7 |
30S ribosomal subunit protein S8 |
30S ribosomal subunit protein S9 |
30S ribosomal subunit protein S10 |
30S ribosomal subunit protein S11 |
30S ribosomal subunit protein S12 |
30S ribosomal subunit protein S13 |
30S ribosomal subunit protein S14 |
30S ribosomal subunit protein S15 |
30S ribosomal subunit protein S16 |
30S ribosomal subunit protein S17 |
30S ribosomal subunit protein S18 |
30S ribosomal subunit protein S19 |
30S ribosomal subunit protein S20 |
Specimen Preparation | |
---|---|
Sample Aggregation State | PARTICLE |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | rapid-freezing in liquid ethane |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 53325 |
Reported Resolution (Å) | 15 |
Resolution Method | FSC 0.5 CUT-OFF |
Other Details | WITH THE USE OF APPROPRIATE STEREOCHEMICAL CONSTRAINTS, AN ATOMIC MODEL FITTED INTO AN EM MAP YIELDS AN ACCURACY OF 5-FOLD BETTER THAN THE NOMINAL RES ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 | ||||
Refinement Space | REAL | ||||
Refinement Protocol | OTHER | ||||
Refinement Target | Minimization of number of poor van der Waals contacts and maximation of correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | REFINEMENT PROTOCOL--CNS implementation of RSRef |
Data Acquisition | |||||||||
---|---|---|---|---|---|---|---|---|---|
Detector Type | KODAK SO-163 FILM | ||||||||
Electron Dose (electrons/Å**2) | 11 |
Imaging Experiment | 1 |
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Date of Experiment | 2004-03-09 |
Temperature (Kelvin) | 93 |
Microscope Model | FEI TECNAI F30 |
Minimum Defocus (nm) | 1.5 |
Maximum Defocus (nm) | 4.3 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | 39000 |
Calibrated Magnification | 39000 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | CNS | |
MODEL FITTING | RSR2000 | |
RECONSTRUCTION | SPIDER |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
CTF correction of 3D-maps by Wiener filtration |