2PT9
The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine and the inhibitor cis-4-methylcyclohexylamine (4MCHA)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2I7C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 288 | 25% PEG3350, 0.1 M Ammonium Sulphate and 0.1 M Bis-Tris pH5.5, 2.5 mM dcAdoMet, 2.5 mM 4MCHA, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 62.75 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 196.24 | ¦Á = 90 |
b = 134.1 | ¦Â = 94.53 |
c = 48.35 | ¦Ã = 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 | mirrors | 2006-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-2 | 1.043 | MAX II | I911-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.2 | 20 | 98.8 | 0.086 | 9.85 | 3.45 | 62364 | 2 | -3 | 39.247 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.5 | 98.8 | 0.346 | 3.8 | 3.45 | 19744 |
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 | 2I7C | 2.2 | 19.77 | -3 | 2 | 60721 | 59243 | 3119 | 93.6 | 0.2 | 0.19831 | 0.19615 | 0.23883 | RANDOM | 35.374 |
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] | |
1.96 | -2.75 | -3.28 | 0.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.529 |
r_dihedral_angle_4_deg | 21.646 |
r_dihedral_angle_3_deg | 16.66 |
r_dihedral_angle_1_deg | 6.382 |
r_scangle_it | 3.157 |
r_scbond_it | 1.963 |
r_angle_refined_deg | 1.46 |
r_mcangle_it | 1.339 |
r_mcbond_it | 0.759 |
r_symmetry_vdw_refined | 0.45 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6744 |
Nucleic Acid Atoms | |
Solvent Atoms | 173 |
Heterogen Atoms | 153 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |