3IOM
Crystal structure of Purine Nucleoside Phosphorylase from Mycobacterium tuberculosis in complex with 2'-Deoxyguanosine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 293 | The protein was cocrystallized with a 1:0.5:1 stoichiometry of 500 mM Na2SO4 (Merck) and 3 mM 2dGuo (Fluka Biochemika), respectively, by hanging-drop vapor diffusion at 18 C. MtPNP protein (1 L of 25 mg mL-1 in 50 mM tris(hydroxymethyl)aminomethane (Tris) pH 7.6) had been previously mixed with an equal volume of the reservoir solution containing 100 mM Tris pH 8.0, 25% poly(ethylene glycol) (PEG) 3350, and 25 mM MgCl2 and hanging drops (3.5 L) were equilibrated against 400 L of the reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.91 | 35.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.48 | α = 90 |
b = 113.48 | β = 90 |
c = 85.011 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | 2009-02-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE D03B-MX1 | 1.42800 | LNLS | D03B-MX1 |
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 | 2.14 | 28.69 | 96.9 | 0.086 | 0.086 | 5.9 | 6.8 | 22411 | 22163 | 2 | 2 | 21.642 |
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 | 2.15 | 2.27 | 81.8 | 0.138 | 0.138 | 3.5 | 6.4 | 625 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1G2O | 2.14 | 28.34 | 2 | 2 | 22163 | 21023 | 1134 | 98.89 | 0.1792 | 0.1792 | 0.17545 | 0.24894 | RANDOM | 18.181 |
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_2_deg | 38.75 |
r_dihedral_angle_4_deg | 20.874 |
r_dihedral_angle_3_deg | 16.849 |
r_dihedral_angle_1_deg | 7.205 |
r_scangle_it | 4.563 |
r_scbond_it | 2.904 |
r_angle_refined_deg | 1.976 |
r_mcangle_it | 1.78 |
r_mcbond_it | 1.023 |
r_nbtor_refined | 0.319 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3792 |
Nucleic Acid Atoms | |
Solvent Atoms | 209 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
AMoRE | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |