5BRF
Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor HPOP-GlcN
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Q2R | PDB entry 2Q2R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 295 | A glucose-free TcGlcK crystal was soaked in 1.0 mM HPOP-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 18% (w/v) PEG 3,350 for 24 hours |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.114 | α = 90 |
b = 80.016 | β = 95.05 |
c = 75.797 | 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 | PIXEL | PSI PILATUS 6M | LR-Design detector positioner | 2014-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97920 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.1 | 50 | 98.5 | 0.067 | 0.078 | 0.039 | 8.2 | 3.5 | 46434 | 44.35 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.1 | 2.18 | 97.4 | 0.389 | 0.46 | 0.242 | 0.792 | 3.2 | 4547 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | THROUGHOUT | PDB entry 2Q2R | 2.102 | 48.395 | 1.37 | 46407 | 2342 | 98.13 | 0.1928 | 0.1905 | 0.2368 | 42.18 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.217 |
f_angle_d | 1.087 |
f_chiral_restr | 0.074 |
f_bond_d | 0.008 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5654 |
Nucleic Acid Atoms | |
Solvent Atoms | 244 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
HKL-2000 | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |