2X0N
Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GD1 | PDB ENTRY 1GD1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | PROTEIN: 5 MICROL OF 6 MG/ML GGAPDH IN 25 MM TRIS HCL PH 7.8, 0.6M AMMONIUM SULPHATE, 2MM NAD, 1MM DITHIOTHREITOL 1MM NA AZIDE, 1 MM EDTA. PRECIPITANT: 5 MICROL OF 52% SATURATED AMMONIUM SULPHATE, 0.2M N,N-BIS-(2-HYDROXYETHYL)-2-AMINOETHANE SULFONIC ACID PH 6.5, 1MM DITHIOTHREITOL, 1MM NA AZIDE, 1MM EDTA, 20MM 3-PHOSPHOGLYCERATE. RESERVOIR: 1 ML |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.27 | 71.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 135.52 | α = 90 |
b = 256.27 | β = 90 |
c = 114.91 | 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 | 273 | FILM | CEA | L | LAUE |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.7 | 0.489-1.905 | SRS | PX9.7 |
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 | 3.2 | 7.4 | 57 | 0.15 | 7.2 | 2.3 | 34991 | 1 | 34.93 |
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 1GD1 | 3.2 | 7.399 | 2.37 | 34991 | 1798 | 57.28 | 0.1533 | 0.1498 | 0.2182 | 34.75 |
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] | |
-4.9115 | -0.717 | -2.7097 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 22.284 |
f_angle_d | 1.492 |
f_chiral_restr | 0.12 |
f_bond_d | 0.009 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16410 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 324 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
DARESBURY | data reduction |
DARESBURY | data scaling |
MERLOT | phasing |
BIOMOL | phasing |