4XSL
Crystal strcutre of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with glycerol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QUL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | 6-9% PEG 4000, 0.1M Sodium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.271 | α = 90 |
b = 124.552 | β = 98.74 |
c = 93.319 | 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 | 100 | CCD | ADSC QUANTUM 210r | 2009-11-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0 | Photon Factory | AR-NW12A |
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 | 1.59 | 50 | 95.4 | 0.066 | 11.8 | 3.1 | 150883 | 14.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1 | 1.59 | 1.62 | 70.9 | 0.351 | 2.8 | 5551 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 2QUL | 1.6 | 32.07 | 145151 | 14471 | 93.6 | 0.181 | 0.178 | 0.205 | RANDOM | 15.2 |
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] | |
-2.33 | -0.98 | -0.04 | 2.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.7 |
c_scangle_it | 2.34 |
c_scbond_it | 1.69 |
c_mcangle_it | 1.46 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.03 |
c_improper_angle_d | 0.82 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9246 |
Nucleic Acid Atoms | |
Solvent Atoms | 1268 |
Heterogen Atoms | 88 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
CNS | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
MOLREP | phasing |