7PTL
Mature conformer of a 6-helix bundle of RNA with clasp
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2D1B |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.002 |
f_angle_d | 1.003 |
f_chiral_restr | 0.06 |
f_plane_restr | 0.007 |
f_bond_d | 0.005 |
Sample |
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Mature conformer of a 6-helix bundle of RNA with clasp |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | LEICA EM GP |
Cryogen Name | ETHANE |
Sample Vitrification Details | 3 microlitre droplet, 4 second delay before blotting, 6 second blot, 0 second delay before plunging. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 337099 |
Reported Resolution (Å) | 4.9 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
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Id | 1 (2D1B) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | Correlation Coefficient | ||||
Overall B Value | 303 | ||||
Fitting Procedure | |||||
Details | Helical templates and tetraloops were generated in RNAbuild. Kissing loops were modelling based on the PDB:2D1B structure. A combination of PHENIX RSR ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 60 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 750 |
Maximum Defocus (nm) | 2500 |
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 | 130000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 3.2.0 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | cryoSPARC | 3.2.0 |
MODEL FITTING | UCSF ChimeraX | 1.2 |
MODEL FITTING | ISOLDE | 1.2 |
MODEL REFINEMENT | PHENIX | 1.19.2-4158-000 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
FINAL EULER ASSIGNMENT | cryoSPARC | 3.2.0 |
CLASSIFICATION | cryoSPARC | 3.2.0 |
RECONSTRUCTION | cryoSPARC | 3.2.0 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | Patch CTF estimation (multi) from cryoSPARC. | 1476537 | Particle picking was performed using the template picker from cryoSPARC with templates generated from an ab initio model from the same dataset. |