5AQ1
Trypanosoma cruzi Glucose-6-phosphate Dehydrogenase in complex with G6P and NADPH
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4E9I | PDB ENTRY 4E9I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | PROTEIN: 2UL TCG6PD 10MG/ML, 5MM G6P, 2 MM NADPH; BUFFER: 20 MM TRIS PH 8.0 WITH 0.2 M NACL AND 5 MM ME PRECIPITANT: 1 UL JEFFAMINE ED-2003 PH 7.0 30%, 0.1 M HEPES PH 7.0; |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.03 | 59.35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 154.946 | α = 90 |
b = 154.946 | β = 90 |
c = 348.358 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 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 | PIXEL | DECTRIS PILATUS 6M | 2015-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | Diamond | I04-1 |
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 | 2.65 | 49.13 | 95.4 | 0.12 | 11.1 | 8.7 | 58510 | 2.5 | 39.6 |
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 | 2.65 | 2.72 | 96.9 | 0.79 | 2.5 | 8.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4E9I | 2.65 | 141.57 | 55569 | 2941 | 94.73 | 0.20118 | 0.19991 | 0.22553 | RANDOM | 47.798 |
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] | |
0.96 | 0.96 | -1.92 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.93 |
r_dihedral_angle_4_deg | 16.075 |
r_dihedral_angle_3_deg | 15.113 |
r_dihedral_angle_1_deg | 5.532 |
r_mcangle_it | 2.725 |
r_scbond_it | 1.804 |
r_mcbond_it | 1.544 |
r_mcbond_other | 1.544 |
r_angle_refined_deg | 1.048 |
r_angle_other_deg | 0.808 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11571 |
Nucleic Acid Atoms | |
Solvent Atoms | 253 |
Heterogen Atoms | 192 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |