3DR2
Structural and Functional Analyses of XC5397 from Xanthomonas campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8 | 297 | 0.1M imidazole pH 8.0, 0.25M Ca(OAc)2, 15% PEG 3350, VAPOR DIFFUSION, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 115.541 | α = 90 |
b = 89.741 | β = 127.71 |
c = 85.228 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 100 | CCD | ADSC QUANTUM 315 | 2007-01-01 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 0.98002, 0.96477, 0.97975 | NSRRC | BL13B1 |
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 | 1.61 | 30 | 97 | 0.29 | 0.038 | 22.9 | 4.7 | 90819 | 2 | 2 | 17 |
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) | ||||||||||
1.61 | 1.67 | 97 | 0.29 | 0.038 | 22.9 | 4.7 | 85371 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||||
X-RAY DIFFRACTION | MAD | 1.67 | 26.78 | 90819 | 14353 | 93.7 | 0.211 | 0.239 | 21.521 |
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] | |
-2.112 | -0.111 | 6.187 | -4.075 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.184 |
c_scbond_it | 1.782 |
c_mcangle_it | 1.644 |
c_angle_d | 1.484 |
c_mcbond_it | 1.387 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4579 |
Nucleic Acid Atoms | |
Solvent Atoms | 626 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SOLVE | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |