Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Single particle cryoEM structure of V. cholerae Type IV competence pilus secretin PilQ
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
13.425
f_angle_d
0.847
f_chiral_restr
0.053
f_bond_d
0.008
f_plane_restr
0.006
Sample
Vibrio cholerae Type IV competence pilus secretin PilQ
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
blot force -6, blot time 4 s
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
100543
Reported Resolution (Å)
2.7
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C14
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
1.5
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
10000
Maximum Defocus (nm)
30000
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
81000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
IMAGE ACQUISITION
SerialEM
CTF CORRECTION
CTFFIND
CTF CORRECTION
RELION
INITIAL EULER ASSIGNMENT
RELION
FINAL EULER ASSIGNMENT
RELION
RECONSTRUCTION
RELION
MODEL REFINEMENT
PHENIX
1.16-dev3549
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
First whole micrograph correction with CtfFind4. Then per particle CTF Refinement in Relion.
252319
CryoSPARC blob picking on 2,510 micrographs yielded 3,100,353 potential particles. After inspection in the cryoSPARC GUI, the 252,319 particles were extracted.