2ZZ9
Structure of aquaporin-4 S180D mutant at 2.8 A resolution by electron crystallography
ELECTRON CRYSTALLOGRAPHY
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 |
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 |