3DGV
Crystal structure of thrombin activatable fibrinolysis inhibitor (TAFI)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NSA | PDB ENTRY 1NSA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 296 | Protein solution: 8 mg/ml protein in 20 mM Tris-HCl, 120 mM NaCl at pH 7.4. reservoir solution: 100 mM Tris-HCl pH 8.0, 1.5 M ammonium sulfate, 2% benzamidine. 10 ul sodium malonate was added to the reservoir the next day after setting up the drop., VAPOR DIFFUSION, Hanging drop, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.45 | 72.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 146.47 | α = 90 |
b = 146.47 | β = 90 |
c = 231.69 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | x-ray | 100 | CCD | ADSC QUANTUM 4 | 2005-05-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | 0.933 | ESRF | ID14-3 |
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 | 2.5 | 90 | 99.2 | 0.122 | 29.2 | 32.2 | 87561 | 86894 | 54.4 |
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 | 2.5 | 2.6 | 95.4 | 0.913 | 4.8 | 30.4 | 9108 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1NSA | 2.5 | 19.86 | 86892 | 4345 | 99.2 | 0.205 | 0.243 | 72.26 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
6.549 | 6.549 | -13.098 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 1.755 |
c_mcangle_it | 1.508 |
c_scbond_it | 1.047 |
c_angle_d | 0.887 |
c_mcbond_it | 0.832 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9621 |
Nucleic Acid Atoms | |
Solvent Atoms | 1019 |
Heterogen Atoms | 375 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
PHASER | phasing |
CNS | refinement |
XDS | data reduction |
XSCALE | data scaling |