3SCZ
Combining crystallographic, thermodynamic, and molecular dynamics studies of Mycobacterium tuberculosis purine nucleoside phosphorylase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | MtPNP:INO:SO4 and MtPNP:HX were crystallized using the experimental conditions described elsewhere. PNP solution was concentrated to 25 mg/mL and co-crystallized with INO:SO4 and HX. Hanging drops were prepared mixing 1 uL of protein solution and 1 uL of reservoir solution (100 mM Tris, pH 8.0, 25 % PEG3350, 25 mM MgCl2), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 115.59 | α = 90 |
b = 115.59 | β = 90 |
c = 86.3 | 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 | MARMOSAIC 325 mm CCD | 2010-02-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE D03B-MX1 | 1.431 | 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 | 1.95 | 21.09 | 100 | 0.099 | 0.099 | 31352 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.95 | 2 | 100 |
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 | THROUGHOUT | 1.95 | 21.09 | 29751 | 1578 | 100 | 0.17635 | 0.17368 | 0.22767 | RANDOM | 17.071 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.075 |
r_dihedral_angle_4_deg | 18.644 |
r_dihedral_angle_3_deg | 15.742 |
r_dihedral_angle_1_deg | 6.608 |
r_scangle_it | 4.043 |
r_scbond_it | 2.644 |
r_angle_refined_deg | 1.806 |
r_mcangle_it | 1.611 |
r_mcbond_it | 0.957 |
r_chiral_restr | 0.134 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3799 |
Nucleic Acid Atoms | |
Solvent Atoms | 282 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
AMoRE | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |