2ZZ9 | pdb_00002zz9

Structure of aquaporin-4 S180D mutant at 2.8 A resolution by electron crystallography

ELECTRON CRYSTALLOGRAPHY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D57

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	6	293	10mM MES (pH 6.0), 75mM NaCl, 50mM MgCl2, 2mM DTT, 1% glycerol, MICRODIALYSIS, temperature 293K

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	Tietz		2008-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE	OTHER	2.8

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	16.89	87	0.197	0.197			10057	8750

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	2.8	2.87	80.15

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	2D57	2.8	10	9879	8089	481	81.88	0.234	0.234	0.23079	0.2448	0.28788	0.2994	RANDOM	52.335

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]
-6.68			-6.68		13.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.615
r_dihedral_angle_3_deg	21.868
r_dihedral_angle_4_deg	18.107
r_dihedral_angle_1_deg	6.297
r_sphericity_free	4.147
r_scangle_it	1.532
r_angle_refined_deg	1.524
r_mcangle_it	1.154
r_scbond_it	0.915
r_sphericity_bonded	0.777
r_rigid_bond_restr	0.731
r_mcbond_it	0.653
r_nbtor_refined	0.321
r_nbd_refined	0.261
r_symmetry_vdw_refined	0.251
r_xyhbond_nbd_refined	0.179
r_symmetry_hbond_refined	0.102
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1642
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	211

Software

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

Sample
aquaporin-4 S180D mutant

Specimen Preparation
Sample Aggregation State	2D ARRAY

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 CCD
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
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details