ELECTRON MICROSCOPY

Sample

HELICAL ASYMMETRIC UNIT OF AN SGRAI DNA-BOUND DIMER

Specimen Preperation
Sample Aggregation State HELICAL ARRAY
Vitrification Instrument HOMEMADE PLUNGER
Cryogen Name ETHANE
Sample Vitrification Details SPECIMENS WERE PREPARED FOR CRYO-EM BY APPLYING 3 MICROLITERS OF SAMPLE IN BINDING BUFFER TO A HOLEY CARBON C-FLAT GRID (CF-2- 2-400) (PROTOCHIPS, INC.) THAT HAD BEEN PLASMA CLEANED (GATAN, SOLARUS) FOR 5 SEC. THE SAMPLE WAS ALLOWED TO ADSORB TO THE GRID FOR 30 SEC., THEN PLUNGE-FROZEN INTO LIQUID ETHANE USING A MANUAL CRYO-PLUNGER AT 4 C.
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 1918
Reported Resolution (Å) 8.6
Resolution Method ?
Other Details WE FIRST CONDUCTED 25 ITERATIONS OF THE IHRSR ROUTINE TO REFINE THE FULL CRYODATA SET AND OBTAIN FINAL HELICAL PARAMETERS -- -86.2 HELICAL TWIST AND 21.6 A RISE. SUBSEQUENTLY, THE MODEL FROM IHRSR WAS USED FOR REFINEMENT IN FREALIGN SPECIFYING DIFFERENT DOSE- -FRACTIONATED STACKS FOR THE REFINEMENT (32 E- PER A2) AND RECONSTRUCTION (16 E- PER A2) ROUTINES. THE FINAL RECONSTRUCTION WAS OBTAINED FROM 1,918 FILAMENT SEGMENTS, AVERAGED 8 TIMES TO ACCOUNT FOR THE HELICAL SYMMETRY BASES WERE OMITTED FROM THE FITTED DNA. ONLY THE PHOSPHATE-SUGAR BACKBONE IS SHOWN. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2441. (DEPOSITION ID: 11901).
Refinement Type
Symmetry Type HELICAL
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details METHOD--DIREX REFINEMENT PROTOCOL--FLEXIBLE
Data Acquisition
Detector Type DIRECT ELECTRON DE-12 (4k x 3k)
Electron Dose (electrons/Å2) 16
Imaging Experiment
Date of Experiment 2012-09-19
Temprature (Kelvin)
Microscope Model FEI TECNAI F20
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 3000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2
Imaging Mode BRIGHT FIELD
Specimen Holder Model .
Nominal Magnification 60000
Calibrated Magnification 41000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
MODEL FITTING DireX ?
RECONSTRUCTION FREALIGN ?
RECONSTRUCTION Xmipp ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
? INDIVIDUAL PARTICLES