2D57 | pdb_00002d57

Double layered 2D crystal structure of AQUAPORIN-4 (AQP4M23) at 3.2 a resolution by electron crystallography

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J4N	PDB ENTRY 1J4N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	dialysys	6	293	10mM MES(pH 6.0), 100mM NaCl, 50mM MgCl2, 2mM DTT, 1% glycerol, dialysys, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69	α = 90
b = 69	β = 90
c = 160	γ = 90

Symmetry
Space Group	P 4 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	electron	4.2	CCD	GATAN ULTRASCAN		2002-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE		0.01968

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	3.2	22.21	87	0.223			6888	5992

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.4	85.8		0.445

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-Factor (All)	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	THROUGHOUT	PDB ENTRY 1J4N	3.2	22.21	6888	5992	337	87	0.286	0.283	0.283	0.2979	0.338	0.3598	RANDOM	53.7

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]
-25.43			-25.43		50.86

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	19.19
c_dihedral_angle_d	19.1
c_mcangle_it	16.9
c_scbond_it	13.55
c_mcbond_it	10.9
c_angle_deg	1.6
c_improper_angle_d	1.1
c_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1659
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
MRC	data reduction
MRC	data scaling
CNS	phasing

Sample
AQUAPORIN 4 CRYSTAL

Specimen Preparation
Sample Aggregation State	2D ARRAY
Embedding Material	trehalose
Embedding Details	7% trehalose

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

Data Acquisition

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
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	diffraction and images

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.