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 6H3C | pdb_00006h3c

Cryo-EM structure of the BRISC complex bound to SHMT2


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GVW 
experimental modelPDB 5V7I 
Sample
BRISC complex bound to SHMT2 alpha
Sample Components
BRISC complex
SHMT2 alpha
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification DetailsA 4 ul sample was applied to the grid and a protocol consisting of 30 s pre-blot incubation, 2 s blotting and no post-blot incubation was utilized for ...A 4 ul sample was applied to the grid and a protocol consisting of 30 s pre-blot incubation, 2 s blotting and no post-blot incubation was utilized for vitrification.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles35595
Reported Resolution (Å)3.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (6GVW, 5V7I)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCorrelation coefficient and
Overall B Value117
Fitting Procedure
DetailsInitial fitting with done using COOT, Rosetta was used for amino acid sequence threading and flexible fitting. COOT and ISOLDE were used for local reb ...Initial fitting with done using COOT, Rosetta was used for amino acid sequence threading and flexible fitting. COOT and ISOLDE were used for local rebuilding. Phenix was used for atom displacement parameter (ADP / B-factor) refinement.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)45
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification58140
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONGautomatch0.53
IMAGE ACQUISITIONEPU1.1.0.30
CTF CORRECTIONRELION2.1
MODEL FITTINGCoot0.8.9
MODEL FITTINGRosetta2018.09.60072
INITIAL EULER ASSIGNMENTRELION2.1
FINAL EULER ASSIGNMENTRELION2.1
CLASSIFICATIONRELION2.1
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTRosetta2018.09.60072
MODEL REFINEMENTPHENIX1.15-3459
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF was determined using GCTF. CTF was corrected within RELION.332598Particles were auto-picked.