ELECTRON MICROSCOPY

Sample

PNEUMOLYSIN

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details PLUNGED INTO ETHANE
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 88
Reported Resolution (Å) 29.00
Resolution Method ?
Other Details RESIDUES 134-142 ARE MISSING FROM THE SEQUENCE. RESIDUES CORRESPONDING TO TO TM1 AND TM2 (187-220,284-315) WERE MODELLED AS A POLY-ALANINE FLAT BETA HAIRPINS. THE OLIGOMER CAN BE GENERATED BY APPLYING 38-FOLD ROTATIONAL SYMMETRY.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space ?
Refinement Protocol RIGID BODY FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details METHOD--THE CRYSTAL STRUCTURE OF PERFRINOGLYSIN O (1PFO, ROSSJOHN ET AL., 1998, CELL 89, 685)WAS PLACED INTO THE CRYO-EM DENSITY MAP (EMD-1107). THE ALPHA CARBON TRACE OF PERFRINGOLYSIN 0 WAS MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO THE POSITION OF ONE SUBUNIT. THE BEST FIT WAS OBTAINED BY SEPARATING THE MONOMER INTO SIX RIGID BODIES- DOMAIN 1(91-172, 231-272 354-373), DOMAIN 2 UPPER (53- 62, 83-90, 374-381), DOMAIN 2 LOWER (63-82, 382-390), DOMAIN 3 (177-186, 221-230, 273-283, 316-353), DOMAIN 3 HAIRPINS (187- 220, 284-315), AND DOMAIN 4 (391-500). THE COMPLETE OLIGOMER (38-MER) WAS GENERATED AND CHECKED FOR CLOSE CONTACTS BOTH BY EYE AND USING THE CCP4 PROGRAM CONTACT.TO IMPROVE THE FIT SECTIONS CORRESPONDING TO 3 SUBUNITS WERE EXTRACTED FROM THE 38-MER MAP (EMD-1107) AND A 44-MER MAP AND ALIGNED. THE WEIGHTED AVERAGE WAS CALCULATED AND THE IMPROVED MAP USED FOR THE FINAL MANUAL FITTING. THE TWO SECTIONS ARE CONSISTENT TO A RESOLUTION OF 28 ANGSTROMS (0.5 CORRELATION FSC) AND THE WEIGHTED AVERAGE MAP WAS RECONSTRUCTED FROM 131 PARTICLES.
Data Acquisition
Detector Type KODAK SO-163 FILM
Electron Dose (electrons/Å2) 20
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TECNAI F20
Minimum Defocus (nm) 1100
Maximum Defocus (nm) 3200
Minimum Tilt Angle (degrees) 0
Maximum Tilt Angle (degrees) 0
Nominal CS 2
Imaging Mode BRIGHT FIELD
Specimen Holder Model .
Nominal Magnification 42000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
? PHASE FLIPPING