4YUZ
Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 5-[(4-methylbenzyl)oxy]quinazoline-2,4-diamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BWB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | PEG4000, ammonium sulfate, bis-Tris |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.531 | α = 90 |
b = 99.665 | β = 91.7 |
c = 134.606 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 90 | CCD | ADSC QUANTUM 270 | 2014-05-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.0 | Photon Factory | AR-NE3A |
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 | 1.97 | 29.73 | 97.62 | 0.149 | 35.5 | 3.4 | 74896 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.97 | 2.024 | 92.7 | 0.254 | 8.5 | 3 |
Refinement
Statistics | |||||||||||||||||||
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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 | 3BWB | 1.97 | 29.73 | 74896 | 3948 | 97.62 | 0.2016 | 0.19902 | 0.24999 | RANDOM | 31.026 |
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] | |
-0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.335 |
r_dihedral_angle_4_deg | 19.309 |
r_dihedral_angle_3_deg | 16.71 |
r_long_range_B_refined | 7.746 |
r_dihedral_angle_1_deg | 6.983 |
r_scbond_it | 4.479 |
r_mcangle_it | 3.947 |
r_mcbond_it | 2.984 |
r_angle_refined_deg | 2.043 |
r_chiral_restr | 0.148 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8674 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms | 138 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |