3IAH
Crystal Structure of Short Chain Dehydrogenase (yciK) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 in Complex with NADP and Acetate.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 295 | Protein solution:0.3M NaCl, 10mM HEPES (pH 7.5); Screen solution: 0.2M Ammonium Acetate, 10mM NADP, 0.1M Bis-Tris (pH 5.5), 25% PEG 3350. , VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 158.664 | α = 90 |
b = 43.302 | β = 93.24 |
c = 71.916 | 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 | MARMOSAIC 300 mm CCD | Beryllium lenses | 2009-06-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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 | 1.83 | 30 | 99.9 | 0.078 | 15.5 | 3.4 | 43678 | 43678 | -3 | 22.1 |
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) | |||||||||||
1 | 1.83 | 1.86 | 100 | 0.353 | 3.2 | 3.1 | 2180 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3G1T | 1.83 | 27.43 | 41212 | 41212 | 2183 | 99.87 | 0.14497 | 0.14497 | 0.14327 | 0.17644 | RANDOM | 14.127 |
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] | |
-1.26 | 0.25 | 2.16 | -0.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.418 |
r_dihedral_angle_4_deg | 10.459 |
r_dihedral_angle_3_deg | 9.168 |
r_scangle_it | 4.49 |
r_scbond_it | 2.828 |
r_dihedral_angle_1_deg | 2.227 |
r_mcangle_it | 1.661 |
r_angle_refined_deg | 1.581 |
r_mcbond_it | 0.945 |
r_angle_other_deg | 0.935 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3925 |
Nucleic Acid Atoms | |
Solvent Atoms | 476 |
Heterogen Atoms | 115 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |