3KBO
2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 295 | Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.3M NDSB-211, 30% PEG 3350, 0.2M Sodium acetate, 0.1M Bis-Tris pH 6.5, 10mm NADP, VAPOR DIFFUSION, HANGING DROP, temperature 295K; Cryo: oil, paratone |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 279.621 | α = 90 |
b = 45.585 | β = 101.58 |
c = 112.335 | 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 225 mm CCD | Beryllium lenses | 2009-09-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.14 | 30 | 98.2 | 0.084 | 27 | 6.6 | 75710 | 75710 | -3 | 34.7 |
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) | |||||||||||
1 | 2.14 | 2.18 | 93.5 | 0.491 | 3.5 | 6 | 3610 |
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 | SAD | THROUGHOUT | 2.14 | 29.93 | 71864 | 71864 | 3806 | 98 | 0.21387 | 0.21387 | 0.21092 | 0.26879 | RANDOM | 27.209 |
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] | |
-1.57 | 0.23 | 5.13 | -3.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.664 |
r_dihedral_angle_3_deg | 11.693 |
r_dihedral_angle_4_deg | 10.682 |
r_scangle_it | 4.87 |
r_scbond_it | 3.469 |
r_dihedral_angle_1_deg | 2.762 |
r_mcangle_it | 2.147 |
r_angle_refined_deg | 1.453 |
r_mcbond_it | 1.286 |
r_angle_other_deg | 0.87 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9900 |
Nucleic Acid Atoms | |
Solvent Atoms | 555 |
Heterogen Atoms | 243 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHENIX | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |