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Fitting result in the O-layer of the subnanometer structure of the bacterial pKM101 type IV secretion system core complex digested with elastase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JQO
Sample TRAN,TRAO AND TRAF COMPLEX ENCODED BY PKM101 DIGESTED WITH 0.02 MG ML- 1 OF ELASTASE FOR 40 MIN AT ROOM TEMPERATURE
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 92, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT 4 SECONDS BEFORE PLUNGING,
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 5430 Reported Resolution (Å) 8.5 Resolution Method Other Details SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2233. (DEPOSITION ID: 11228). Refinement Type Symmetry Type POINT Point Symmetry C14
Map-Model Fitting and Refinement Id 1 (3JQO) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Cross-correlation coefficient Overall B Value Fitting Procedure Details METHOD--RIGID BODY FOLLOWED BY FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY
Data Acquisition Detector Type GENERIC GATAN Electron Dose (electrons/Å**2) 20
Imaging Experiment 1 Date of Experiment 2012-01-11 Temperature (Kelvin) 95 Microscope Model FEI TECNAI 12 Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.1 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 66000 Calibrated Magnification 68100 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details 4000X4000 CCD
EM Software Task Software Package Version MODEL FITTING Flex-EM MODEL FITTING Sculptor MODEL FITTING Situs MODEL FITTING UCSF Chimera RECONSTRUCTION IMAGIC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING, EACH CCD IMAGE