Experiment: 5K10

Cryo-EM structure of isocitrate dehydrogenase (IDH1)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MAP

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.616
f_angle_d	0.915
f_chiral_restr	0.056
f_bond_d	0.009
f_plane_restr	0.005

Sample
isocitrate dehydrogenase R132C mutant

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Plunged into liquid ethane (LEICA EM GP)

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	49936
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The primary map for this entry corresponds to the uncorrected reconstruction. A version sharpened using a B-factor of -180 is provided as additional v ...	The primary map for this entry corresponds to the uncorrected reconstruction. A version sharpened using a B-factor of -180 is provided as additional volume data. The reconstruction, obtained without imposing symmetry, is also provided with this entry as additional volume data.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (3MAP)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	270000
Calibrated Magnification	101000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	FREALIGN	9.10
MODEL FITTING	UCSF Chimera
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
INITIAL EULER ASSIGNMENT	FREALIGN	9.10
FINAL EULER ASSIGNMENT	FREALIGN	9.10
RECONSTRUCTION	FREALIGN	9.10

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		499184