9EUV | pdb_00009euv

Lymphostatin, conformation 1 (composite structure)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.445
f_angle_d	0.429
f_chiral_restr	0.039
f_plane_restr	0.004
f_bond_d	0.002

Sample
Lymphostatin

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	120944
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details	This is a composite map from two original maps. One overall map was used until residue 2199 and for overall alignment. The second map was a local refinement for the C-terminal part from residue 2200. Phenix Combine focused maps tool was used (version 1.20.1)
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	70

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	1400
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.4
IMAGE ACQUISITION	EPU	3.5
CTF CORRECTION	cryoSPARC	4.4
MODEL FITTING	Coot	0.9.8
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC	4.4
RECONSTRUCTION	RELION	5.0
MODEL REFINEMENT	PHENIX	1.20.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		13373262