2D57
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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1J4N | PDB ENTRY 1J4N |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.96 | 58.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69 | α = 90 |
b = 69 | β = 90 |
c = 160 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ELECTRON MICROSCOPE | 0.01968 |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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[2][2] | Anisotropic B[3][3] | ||||
-25.43 | -25.43 | 50.86 |
RMS Deviations | |
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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 | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1659 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MRC | data reduction |
MRC | data scaling |
CNS | phasing |
Sample |
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AQUAPORIN 4 CRYSTAL |
Specimen Preparation | |
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Sample Aggregation State | 2D ARRAY |
Embedding Material | trehalose |
Embedding Details | 7% trehalose |
3D Reconstruction | |
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Reconstruction Method | CRYSTALLOGRAPHY |
Number of Particles | |
Reported Resolution (Å) | |
Resolution Method | |
Other Details | |
Refinement Type | |
Symmetry Type | 2D CRYSTAL |
Data Acquisition |
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Imaging Experiment | 1 |
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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 |