3PP8
2.1 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KBO |
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: 0.2M Sodium acetate, 0.1M Bis-Tris (pH 6.5), 0.01M Glycolic acid, 30% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.495 | α = 90 |
b = 139.371 | β = 90 |
c = 111.043 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 2010-10-21 | 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 | 2.1 | 30 | 99.9 | 0.074 | 39.3 | 6.1 | 18836 | 18836 | -3 | 36 |
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) | |||||||||||
2.1 | 2.14 | 100 | 0.486 | 3.8 | 6.2 | 924 |
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 | 3KBO | 2.1 | 29.51 | 17835 | 17835 | 967 | 99.84 | 0.19865 | 0.19865 | 0.19659 | 0.23508 | RANDOM | 44.491 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.95 | -0.72 | 1.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.6 |
r_dihedral_angle_4_deg | 14.205 |
r_dihedral_angle_3_deg | 13.422 |
r_scangle_it | 4.972 |
r_scbond_it | 3.565 |
r_dihedral_angle_1_deg | 3.508 |
r_mcangle_it | 2.144 |
r_angle_refined_deg | 1.396 |
r_mcbond_it | 1.314 |
r_angle_other_deg | 0.816 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2449 |
Nucleic Acid Atoms | |
Solvent Atoms | 82 |
Heterogen Atoms |
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 |