2PKW
Crystal structure of UPF0341 protein yhiQ from Salmonella typhimurium, Northeast Structural Genomics Consortium Target StR221
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH UNDER OIL | 8 | 291 | 2 micro-L of protein solution containing 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT was mixed with equal volume of 100 mM Tris-HCl pH 8.0, 40% PEG 1000, and 100 mM Magnesium acetate, MICROBATCH UNDER OIL, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.967 | α = 90 |
b = 70.248 | β = 90 |
c = 77.788 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | ADSC QUANTUM 210 | mirrors | 2007-04-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | 0.97880 | NSLS | X12C |
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 | 2.1 | 28.53 | 99.6 | 0.068 | 0.053 | 28.1 | 6.6 | 25710 | 25710 | 16.2 |
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) | ||||||||||
2.1 | 2.18 | 99.5 | 0.329 | 0.317 | 4 | 6 | 2532 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 2.1 | 28.53 | 2 | 25710 | 23015 | 2152 | 89 | 0.209 | 0.208 | 0.208 | 0.259 | RANDOM | 32.5 |
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] | |
-0.94 | 4.37 | -3.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.8 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.85 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1934 |
Nucleic Acid Atoms | |
Solvent Atoms | 144 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
ADSC | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SnB | phasing |
RESOLVE | phasing |