3D9S
Human Aquaporin 5 (AQP5) - High Resolution X-ray Structure
X-RAY DIFFRACTION
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 | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 281 | 19% polyethylene glycol 400, 0.1M Tris HCl pH 7.6, 0.1M NaCl, 6% v/v 1,6-hexanediol, 3% v/v 1,4-butanediol or 3% v/v 1,3-propanediol, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.15 | 61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.477 | α = 90 |
b = 90.644 | β = 90 |
c = 184.395 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | x-ray | 170 | CCD | ADSC QUANTUM 4 | 2007-07-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | 0.931 | ESRF | ID14-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 52.56 | 82.9 | 0.061 | 8.3 | 3.7 | 84751 | 84751 | 3 | 26.15 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2 | 2.11 | 82.6 | 0.494 | 1.5 | 3.7 | 12232 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | AB INITIO | FREE R | PDB ENTRY 1J4N | 2 | 10 | 4 | 84751 | 79673 | 4174 | 78 | 0.162 | 0.193 | THIN RESOLUTION SHELLS (RANDOMLY) TO ACCOUNT FOR TWINNING; TWIN RELATED REFLECTIONS ALWAYS IN THE SAME SET (WORK OR TEST SET) NOT DIVIDED BETWEEN THEM. | 37.2 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
7386.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_similar_adp_cmpnt | 0.103 |
s_non_zero_chiral_vol | 0.035 |
s_zero_chiral_vol | 0.033 |
s_from_restr_planes | 0.0241 |
s_angle_d | 0.024 |
s_anti_bump_dis_restr | 0.013 |
s_bond_d | 0.006 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7241 |
Nucleic Acid Atoms | |
Solvent Atoms | 111 |
Heterogen Atoms | 38 |
Software
Software | |
---|---|
Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
MxCuBE | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |