3TVL
Complex between the human thiamine triphosphatase and triphosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BHD | PDB entry 3BHD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.2 | 293 | O.1 citrate, 0.2 Ammonium sulfate, triphosphate 0.1M, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.93 | 36.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.378 | α = 90 |
b = 63.529 | β = 108.75 |
c = 70.95 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | CCD | ADSC QUANTUM 315 | 2010-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.9797 | ESRF | BM30A |
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 | 2.3 | 46.2 | 94.8 | 0.099 | 9 | 3.2 | 16547 | 16547 |
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 | 2.3 | 2.42 | 78.2 | 0.45 | 2.6 | 3.1 | 1979 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MIR | THROUGHOUT | PDB entry 3BHD | 2.3 | 46.16 | 15702 | 15702 | 832 | 94.5 | 0.18429 | 0.18429 | 0.18038 | 0.26085 | RANDOM | 28.326 |
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] | |
-0.17 | 0.44 | 0.92 | -0.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.389 |
r_dihedral_angle_4_deg | 17.373 |
r_dihedral_angle_3_deg | 16.843 |
r_dihedral_angle_1_deg | 6.37 |
r_scangle_it | 4.845 |
r_mcangle_it | 3.745 |
r_scbond_it | 3.173 |
r_mcbond_it | 2.3 |
r_angle_refined_deg | 1.574 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3160 |
Nucleic Acid Atoms | |
Solvent Atoms | 95 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
AMoRE | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |