2X0S
3.0 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOSOMAL PYRUVATE PHOSPHATE DIKINASE FROM TRYPANOSOMA BRUCEI
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DIK | PDB ENTRY 1DIK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.8 | HANGING DROP, 2 MICROLITER PROTEIN AND 2 MICROLITER PRECIPITANT SOLUTION. PROTEIN SOLUTION. 50 MG/ML, 20 MM IMIDAZOLE PH 7.0, 100 MM NACL, 100 MM MGCL2, 20% (V/V) GLYCEROL. PRECIPITANT SOLUTION. 0.1 M BICINE PH 8.8, 1.5 % (W/V) PEG 5000 MONOMETHYLETHER, 10 % (V/V) GLYCEROL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.17 | α = 90 |
b = 153.5 | β = 90 |
c = 65.46 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | 277 | IMAGE PLATE | MARRESEARCH | 2000-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LURE BEAMLINE DW32 | LURE | DW32 |
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 | 24 | 96 | 0.09 | 14.8 | 5.3 | 24120 | 61 |
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 | 3.1 | 88.6 | 0.28 | 3.1 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1DIK | 2.997 | 23.938 | 1.62 | 24115 | 1163 | 95.73 | 0.1687 | 0.1649 | 0.2415 | 81.08 |
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] | |
6.1816 | -1.6729 | -4.8838 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.423 |
f_angle_d | 1.345 |
f_chiral_restr | 0.082 |
f_bond_d | 0.009 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6935 |
Nucleic Acid Atoms | |
Solvent Atoms | 36 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
BIOMOL | data scaling |
CNS | phasing |