7PEO
Structure of the Caulobacter crescentus S-layer protein RsaA N-terminal domain bound to LPS and soaked with Holmium
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6T72 |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 42.751 |
r_dihedral_angle_2_deg | 37.367 |
r_mcangle_it | 29.166 |
r_dihedral_angle_4_deg | 24.997 |
r_scbond_it | 22.677 |
r_mcbond_it | 17.993 |
r_dihedral_angle_3_deg | 16.497 |
r_dihedral_angle_1_deg | 6.471 |
r_angle_refined_deg | 1.228 |
r_chiral_restr | 0.102 |
Sample |
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Structure of the Caulobacter crescentus S-layer protein RsaA N-terminal domain bound to LPS and soaked with Holmium |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | Vitrobot options: Blot time 4 seconds, Blot force -13,1, Wait time 10 seconds, Drain time 0.5 seconds, |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 158430 |
Reported Resolution (Å) | 4.37 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | The final map was obtained from 158,430 particles and post-processed using a soft mask focused on the inner fourteen subunits yielding a resolution of ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C1 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (6T72) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | The atomic coordinates (PDB ID 6T72) of our previous cryo-EM structure (von Kugelgen et al., 2020) of the RsaANTD oligomer bound to the O-antigen of l ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 44.8 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | -1000 |
Maximum Defocus (nm) | -4000 |
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 | 130000 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | EPU software |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | RELION | 3.0 |
IMAGE ACQUISITION | EPU | |
CTF CORRECTION | CTFFIND | 4.1.13 |
MODEL FITTING | UCSF Chimera | 1.13 |
INITIAL EULER ASSIGNMENT | RELION | 3.0 |
FINAL EULER ASSIGNMENT | RELION | 3.0 |
CLASSIFICATION | RELION | 3.0 |
RECONSTRUCTION | RELION | 3.0 |
MODEL REFINEMENT | REFMAC | 5.8.0258 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | RELION refinement with in-built CTF correction. The function is similar to a Wiener filter, so amplitude correction included. | 545533 | Initial Particles were extracted in a 2x down-sampled 150 pixel x 150 pixel box and classified using reference-free 2D-classification inside RELION 3.0. |