4C3G | pdb_00004c3g

cryo-EM structure of activated and oligomeric restriction endonuclease SgrAI


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DVO 
Sample
HELICAL ASYMMETRIC UNIT OF AN SGRAI DNA-BOUND DIMER
Specimen Preparation
Sample Aggregation StateHELICAL ARRAY
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsSPECIMENS 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 ...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 MethodSINGLE PARTICLE
Number of Particles1918
Reported Resolution (Å)8.6
Resolution Method
Other DetailsWE FIRST CONDUCTED 25 ITERATIONS OF THE IHRSR ROUTINE TO REFINE THE FULL CRYODATA SET AND OBTAIN FINAL HELICAL PARAMETERS -- -86.2 HELICAL TWIST AND 2 ...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 TypeHELICAL
Map-Model Fitting and Refinement
Id1 (3DVO)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsMETHOD--DIREX REFINEMENT PROTOCOL--FLEXIBLE
Data Acquisition
Detector TypeDIRECT ELECTRON DE-12 (4k x 3k)
Electron Dose (electrons/Å**2)16
Imaging Experiment1
Date of Experiment2012-09-19
Temperature (Kelvin)
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification60000
Calibrated Magnification41000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGDireX
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONXmipp
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
INDIVIDUAL PARTICLES