8SJX
Structure of lens aquaporin-0 array in sphingomyelin/cholesterol bilayer (2SM:1Chol)
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2B6O |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.5 | α = 90 |
b = 65.5 | β = 90 |
c = 200 | γ = 90 |
Symmetry | |
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Space Group | P 4 2 2 |
Data Collection
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
ELECTRON CRYSTALLOGRAPHY | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.5 | 2.5 | 1.33 | 16437 | 1643 | 86.71 | 0.2622 | 0.2595 | 0.2863 | Random selection | 66.6 |
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 | 18.3187 |
f_angle_d | 1.0919 |
f_chiral_restr | 0.0395 |
f_bond_d | 0.0084 |
f_plane_restr | 0.0054 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHASER | phasing |
IPLT | data reduction |
Sample |
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Lens aquaporin-0 in sphingomyelin/cholesterol bilayer |
Specimen Preparation | |
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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 | |
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Reconstruction Method | CRYSTALLOGRAPHY |
Number of Particles | |
Reported Resolution (Å) | 2.5 |
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 |
Map-Model Fitting and Refinement | |||||
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Id | 1 (2B6O) | ||||
Refinement Space | |||||
Refinement Protocol | |||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details |
Data Acquisition | |||||||||
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Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 10 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE |