5K0Z | pdb_00005k0z

Cryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound state

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I0Z

Sample
Lactate dehydrogenase (LDH) in complex with GSK2837808A

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	50865
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The primary map in this entry corresponds to the uncorrected reconstruction. A version sharpened using a B-factor of -150 is provided as additional volume data.
Refinement Type
Symmetry Type	POINT
Point Symmetry	D2

Map-Model Fitting and Refinement
Id	1 (1I0Z)
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)	800
Maximum Defocus (nm)	2200
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		508402