8SJY | pdb_00008sjy

Structure of lens aquaporin-0 array in sphingomyelin/cholesterol bilayer (1SM:2Chol)

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B6O

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.5	α = 90
b = 65.5	β = 90
c = 200	γ = 90

Symmetry
Space Group	P 4 2 2

Data Collection

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	2.5	1.33	17031	1704	90.19	0.2642	0.2617	0.2823	0.2866	0.3053	Random selection	51.15

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.071
f_angle_d	0.8381
f_chiral_restr	0.0374
f_bond_d	0.0053
f_plane_restr	0.0046

Software

Software
Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement
PHASER	phasing
IPLT	data reduction

Sample
Lens aquaporin-0 in sphingomyelin/cholesterol bilayer

Specimen Preparation
Sample Aggregation State	2D ARRAY
Embedding Material	Trehalose
Embedding Details	Aquaporin-0 2D crystals were prepared on molybdenum grids using the carbon sandwich method and a trehalose concentration ranging from 3% to 5% (w/v).

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	2.35
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	2D CRYSTAL
Space Group Name	P 4 2 2
Length a	65.5
Length b	65.5
Angle Gamma	90
Space Group Name	P 4 2 2
Length a	65.5
Length b	65.5
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (2B6O)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	10

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model	OTHER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	The diffraction patterns were recorded without setting defocus.

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	DigitalMicrograph	2
MOLECULAR REPLACEMENT	CCP4 package	6.0
CRYSTALLOGRAPHY MERGING	IPET	0.9.8
RECONSTRUCTION	IPET	0.9.8
MODEL REFINEMENT	CNS	1.3
MODEL REFINEMENT	PHENIX	1.20.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.