2O07
Human spermidine synthase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 300 | 20% PEG 3350, 0.2M Mg(OAc)2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.21 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 58.125 | ¦Á = 90 |
b = 60.663 | ¦Â = 108.68 |
c = 86.705 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU | 2006-03-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.54178 |
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 | 1.89 | 82.2 | 97.9 | 0.088 | 0.119 | 4.4 | 44511 | 44511 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.89 | 82.2 | 42238 | 2255 | 97.15 | 0.17906 | 0.17647 | 0.22751 | RANDOM | 22.497 |
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] | |
0.99 | -0.42 | -0.2 | -1.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.417 |
r_dihedral_angle_4_deg | 17.5 |
r_dihedral_angle_3_deg | 13.386 |
r_dihedral_angle_1_deg | 6.671 |
r_scangle_it | 3.54 |
r_scbond_it | 2.403 |
r_angle_refined_deg | 1.562 |
r_mcangle_it | 1.394 |
r_mcbond_it | 0.894 |
r_nbtor_refined | 0.3 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4427 |
Nucleic Acid Atoms | |
Solvent Atoms | 624 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |