3VNC
Crystal Structure of TIP-alpha N25 from Helicobacter Pylori in its natural dimeric form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 293 | 16% PEG3350, 80% Tacsimate, 2% 1,2-propanediol, 5% MPD, 5% Glycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.32 | 62.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 138.7 | α = 90 |
b = 46.936 | β = 127.78 |
c = 99.1 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 90 | CCD | ADSC QUANTUM 315r | 2009-10-26 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.97898, 0.97917, 0.96395 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.6 | 49.14 | 95.4 | 0.102 | 0.102 | 17.7 | 7.2 | 15779 | 15054 | 37.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.6 | 2.74 | 99.9 | 0.374 | 0.374 | 4.7 | 7.3 | 2289 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.6 | 49.14 | 15815 | 15054 | 1527 | 95.1 | 0.231 | 0.231 | 0.264 | RANDOM | 48.7 |
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] | |
12.88 | 11.46 | -16.65 | 3.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.6 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.78 |
c_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2382 |
Nucleic Acid Atoms | |
Solvent Atoms | 55 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SOLVE | phasing |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |