3JD5
Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 9.401 |
f_angle_d | 0.304 |
f_chiral_restr | 0.028 |
f_plane_restr | 0.003 |
f_bond_d | 0.001 |
Sample |
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small subunit of mitochondrial ribosome |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK I |
Cryogen Name | ETHANE |
Sample Vitrification Details | Plunged into liquid ethane (FEI VITROBOT MARK I). |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 307556 |
Reported Resolution (Å) | 7 |
Resolution Method | |
Other Details | A total of 866553 particle images were picked and subjected to supervised classification. Based on statistical information derived from Relion classi ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (5AJ3, 3J9M) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Cross-correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | METHOD--Flexible fitting REFINEMENT PROTOCOL--rigid body |
Data Acquisition | |||||||||
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Detector Type | GATAN ULTRASCAN 1000 (2k x 2k) | ||||||||
Electron Dose (electrons/Å**2) | 9 |
Imaging Experiment | 1 |
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Date of Experiment | 2009-10-10 |
Temperature (Kelvin) | 100 |
Microscope Model | JEOL 3200FS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 4500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | GATAN LIQUID NITROGEN |
Nominal Magnification | 60000 |
Calibrated Magnification | 59717 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | MDFF | |
RECONSTRUCTION | RELION | 1.2 |
RECONSTRUCTION | SPIDER |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
CTFFIND3 |