3QV7
Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with ponceau S and acid blue 25.
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 |
3.82 | 67.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 182.109 | α = 90 |
b = 164.798 | β = 115.8 |
c = 123.348 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 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 | 2.7 | 21.14 | 100 | 0.123 | 0.144 | 10.2 | 3.7 | 89354 | 2.7 | 2.7 | 56.4 |
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 | 2.7 | 2.85 | 100 | 0.542 | 0.64 | 2.1 | 3.5 | 12910 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.7 | 21.14 | 84872 | 4480 | 99.77 | 0.21677 | 0.21535 | 0.24414 | RANDOM | 45.246 |
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] | |
0.39 | 0.44 | -0.23 | 0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.249 |
r_dihedral_angle_3_deg | 14.122 |
r_dihedral_angle_4_deg | 14.023 |
r_dihedral_angle_1_deg | 4.233 |
r_angle_refined_deg | 0.859 |
r_scangle_it | 0.749 |
r_mcangle_it | 0.428 |
r_scbond_it | 0.4 |
r_mcbond_it | 0.232 |
r_chiral_restr | 0.055 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13572 |
Nucleic Acid Atoms | |
Solvent Atoms | 505 |
Heterogen Atoms | 270 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |