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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
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
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 ...
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 4.37 A according to the gold standard Fourier shell correlation criterion of 0.143 (Scheres, 2012) with some anisotropy in Z as judged by directional FSCs (Tan et al., 2017)
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
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 ...
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 lipopolysaccharide (LPS) were rigid body fitted into the final post-processed map from Relion 3.0 (Zivanov et al., 2018) using UCSF Chimera (Pettersen et al., 2004). The resulting fitted model was subjected to real-space refinement using Refmac5 (Murshudov et al., 2011) inside the CCP-EM suite (Burnely et al., 2017), as described previously (von Kugelgen et al., 2020), using reference restraints of the initial structure (PDB ID 6T72) generated with PROSMART (Nicholls et al. 2012).
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
44.8
Imaging Experiment
1
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
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
MODEL REFINEMENT
PHENIX
Image Processing
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.