7S2N
Crystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in the apo form (open conformation)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Q2R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | 1.0 uL of 7.4 mg/mL TcGlcK(F337L) in buffered solution [50 mM HEPES (pH 7.5), 0.2 M imidazole, 2 mM magnesium chloride] + 1.0 uL of precipitant solution [14% (w/v) PEG 3350, 0.1 M sodium citrate tribasic] was equilibrated against 85 uL of the precipitant solution using a 96-well sitting-drop plate (Innovadyne) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 49.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.75 | α = 90 |
b = 78.985 | β = 101.17 |
c = 77.567 | 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 315r | 2014-06-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 0.9792 | APS | 14-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.75 | 40 | 99.9 | 0.059 | 0.031 | 32.7 | 3.8 | 80560 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.75 | 1.78 | 100 | 0.774 | 0.4 | 0.688 | 2 | 3.7 |
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 | 2Q2R | 1.75 | 39.69 | 76581 | 3956 | 99.35 | 0.1622 | 0.1607 | 0.1911 | RANDOM | 34.491 |
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] | |
0.5 | -0.42 | -0.24 | -0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.848 |
r_dihedral_angle_4_deg | 13.406 |
r_dihedral_angle_3_deg | 11.948 |
r_dihedral_angle_1_deg | 6.267 |
r_angle_other_deg | 2.316 |
r_angle_refined_deg | 1.715 |
r_chiral_restr | 0.091 |
r_bond_other_d | 0.035 |
r_gen_planes_other | 0.019 |
r_bond_refined_d | 0.013 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5675 |
Nucleic Acid Atoms | |
Solvent Atoms | 729 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |