1SU1
Structural and biochemical characterization of Yfce, a phosphoesterase from E. coli
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | drop: 50 mM sodium Cacodylate pH 6.5, 5 mM Hepes pH 7.5, 0.1 M Ammonium sulfate, 10% PEG 4000, 0.25 M NaCl, 1 mM BME, 5 mg/ml protein; well: 0.1 M sodium Cacodylate pH 6.5, 0.2 M Ammonium sulfate, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.02 | α = 90 |
b = 71.02 | β = 90 |
c = 173.68 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 | 170 | CCD | MARRESEARCH | Si 111 | 2003-10-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | 0.979438 | APS | 5ID-B |
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 | 100 | 0.095 | 5.9 | 5.7 | 48352 | 6 | 6 | 28.7 |
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) | |||||||||||
2.2 | 2.32 | 100 | 0.294 | 2.5 | 5.7 | 7059 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SIRAS | THROUGHOUT | 2.25 | 20 | 46454 | 46449 | 2361 | 100 | 0.215 | 0.213 | 0.213 | 0.252 | RANDOM | 37.1 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25.1 |
c_angle_d | 1.5 |
c_improper_angle_d | 0.99 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5649 |
Nucleic Acid Atoms | |
Solvent Atoms | 362 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SOLVE | phasing |
CNS | refinement |
CCP4 | data scaling |