2B6O | pdb_00002b6o

Electron crystallographic structure of lens Aquaporin-0 (AQP0) (lens MIP) at 1.9A resolution, in a closed pore state

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SOR	1SOR - aquaporin-0 (MIP) strructure determined by electron crystallography

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	6	300	20mM MES pH 6.0, 50mM MgCl2, 5mM DTT, MICRODIALYSIS, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.5	α = 90
b = 65.5	β = 90
c = 160	γ = 90

Symmetry
Space Group	P 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	electron	281	CCD	GATAN	4k X 4k	2003-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE	JEM3000SFF

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.9	20	80	0.166		5.7					18.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	70.5			2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	THROUGHOUT	1SOR - aquaporin-0 (MIP) strructure determined by electron crystallography	1.9	5	16180	14600	1580		0.258	0.2853	0.299	0.3206	RANDOM	58.4

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]
-7.32			-7.32		14.64

RMS Deviations
Key	Refinement Restraint Deviation
o_dihedral_angle_d	19.8
o_mcangle_it	2.61
o_scangle_it	2.44
o_angle_deg	1.9
o_scbond_it	1.63
o_mcbond_it	1.53
o_improper_angle_d	1.25
o_bond_d	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1783
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	349

Software

Software
Software Name	Purpose
GATAN	data collection
GATAN	data reduction
CNS	refinement
GATAN	data scaling
CNS	phasing

Sample
aquaporin-0

Specimen Preparation
Sample Aggregation State	2D ARRAY
Vitrification Instrument
Cryogen Name	NITROGEN
Sample Vitrification Details
Embedding Material	trehalose
Embedding Details	10% trehalose

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
Resolution Method
Other Details
Refinement Type
Symmetry Type	2D CRYSTAL

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

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL 3000SFF
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model	JEOL
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	CNS	1.1
RECONSTRUCTION	MRC

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.