5VRF | pdb_00005vrf

CryoEM Structure of the Zinc Transporter YiiP from helical crystals

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3J1Z

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.765
f_angle_d	1.274
f_chiral_restr	0.056
f_bond_d	0.011
f_plane_restr	0.008

Sample
YiiP dimer in an inward-facing conformation

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	72333
Reported Resolution (Å)	4.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Reconstruction was achieved using the IHRSR method implemented in RELION 2.0.
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	D5
Axial Rise	28.2
Angular Rotation	-17

Map-Model Fitting and Refinement
Id	1 (3J1Z, 3J1Z)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	The residues were manually adjusted in COOT relying on the large side-chain residues, and the whole system was further optimized using the real_space_refine algorithm in Phenix to ensure proper fit. The conformation was subjected to 13 rounds of COOT/Phenix refinements.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (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)	1200
Maximum Defocus (nm)	2500
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	22500
Calibrated Magnification
Source	LAB6
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	SPARX/EMAN2	EMAN2.1
PARTICLE SELECTION	RELION	2.0
IMAGE ACQUISITION	Leginon
CTF CORRECTION	CTFFIND	4.1
CTF CORRECTION	Gctf	0.50
MODEL FITTING	Coot	0.8.6
INITIAL EULER ASSIGNMENT	RELION	2.0
FINAL EULER ASSIGNMENT	RELION	2.0
CLASSIFICATION	RELION	2.0
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	PHENIX	1.11

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		141904	2293 filaments selected with SPARX/EMAN2, then windowed into 141,904 segments (450x450 pixel overlapping segments)