3W1I
Crystal structure of the N-terminal truncated selenocysteine synthase SelA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 120mM Tris-HCl, 11% PEG 4000, 400mM CaCl2, 160mM KCl, 5.0mM NiCl2, 50mM Na2S2O3, 50mM L-serine, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.825 | α = 90 |
b = 280.936 | β = 113.45 |
c = 97.645 | 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 | mirrors | 2008-03-04 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 90 | CCD | ADSC QUANTUM 315 | mirrors | 2008-02-19 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 1.07117 | Photon Factory | BL-17A |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.97917, 0.97947 | SPring-8 | BL41XU |
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 | 3.192 | 50 | 99.5 | 0.09 | 0.09 | 22.4 | 7.4 | 75523 | 75145 | -2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.2 | 3.31 | 96 | 0.674 | 0.674 | 2.5 | 6.2 | 7513 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | MAD | 3.192 | 48.941 | 1.35 | 75789 | 75046 | 3750 | 99.02 | 0.1769 | 0.1738 | 0.2354 | RANDOM | 130.1176 |
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] | |
-21.7714 | -6.6801 | -9.6703 | 31.4417 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.459 |
f_angle_d | 1.22 |
f_chiral_restr | 0.071 |
f_bond_d | 0.009 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 30712 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
DM | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
autoSHARP | phasing |