8J7C
Crystal structure of triosephosphate isomerase from Leishmania orientalis at 1.88A with an arsenic ion bound at Cys57
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.9 | 291.15 | Equal volumes (1.0 microliter) of enzyme (24.2 mg/ml in 50 mM potassium phosphate buffer, pH 8.0, containing 50 mM KCl, 5 mM DTT, and 10% glycerol) and precipitant (PEG8000 18% w/v in 0.2 mM calcium acetate hydrate, 0.1 M and sodium cacodylate trihydrate, pH 5.9) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.44 | α = 90 |
b = 76.45 | β = 101.14 |
c = 94.94 | 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 | 100 | CCD | MAR CCD 165 mm | spherical mirror for CM and toroidal mirror for M | 2015-05-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLRI BEAMLINE BL7.2W | 1.5500 | SLRI | BL7.2W |
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) | CC (Half) | 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 | 1.88 | 21.56 | 98.6 | 0.082 | 0.101 | 0.059 | 0.991 | 11.9 | 2.8 | 46160 | 6.92 |
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 | 1.88 | 1.92 | 81.2 | 0.549 | 0.682 | 0.399 | 0.598 | 2.4 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FREE R-VALUE | 1.88 | 19.98 | 43811 | 2354 | 99.06 | 0.17366 | 0.17148 | 0.21377 | RANDOM | 16.047 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 13.959 |
r_dihedral_angle_1_deg | 7.052 |
r_dihedral_angle_2_deg | 5.926 |
r_long_range_B_refined | 4.584 |
r_long_range_B_other | 4.322 |
r_scangle_other | 2.966 |
r_scbond_it | 1.897 |
r_scbond_other | 1.897 |
r_mcangle_it | 1.881 |
r_mcangle_other | 1.881 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3712 |
Nucleic Acid Atoms | |
Solvent Atoms | 491 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
pointless | data scaling |
MOSFLM | data reduction |
PHASER | phasing |