3QV8
Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with benzothiazole-2,5-disulfonic acid.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PKL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 277 | 7-16% PEG 8,000, 20 mM TEA buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10-25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.554 | α = 90 |
b = 131.282 | β = 90 |
c = 167.602 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | CCD | ADSC QUANTUM 315 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.45 | 44.41 | 100 | 0.095 | 0.102 | 16.1 | 7.3 | 360184 | 49123 | 2.45 | 2.45 | 52.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.45 | 2.58 | 100 | 0.563 | 0.605 | 4.1 | 7.5 | 7089 |
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 | 1PKL | 2.45 | 44.41 | 46606 | 2485 | 99.9 | 0.23608 | 0.23448 | 0.26576 | RANDOM | 52.196 |
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] | |
-1.13 | 3.92 | -2.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.004 |
r_dihedral_angle_4_deg | 16.723 |
r_dihedral_angle_3_deg | 16.33 |
r_dihedral_angle_1_deg | 5.672 |
r_scangle_it | 2.448 |
r_scbond_it | 1.401 |
r_angle_refined_deg | 1.259 |
r_mcangle_it | 1.019 |
r_mcbond_it | 0.536 |
r_chiral_restr | 0.079 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6748 |
Nucleic Acid Atoms | |
Solvent Atoms | 211 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |