3RD5
Crystal structure of a putative uncharacterized protein from Mycobacterium Paratuberculosis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | EMERALDBIOSYSTEMS JCSG+ SCREEN B4: 100MM HEPES PH 7.5, 10% PEG 8000, 8% ETHYLENE GLYCOL, MYPAA.01249.CA1 PW29465 AT 29 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K. |
2 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | EMERALDBIOSYSTEMS JCSG+ SCREEN B4: 100MM HEPES PH 7.5, 10% PEG 8000, 8% ETHYLENE GLYCOL, MYPAA.01249.CA1 PW29465 AT 29 MG/ML, FOR PHASING THIS CRYSTAL WAS TRANFERRED IN 100MM HEPES PH 7.5, 15% PEG 6000, 10% ETHYLENE GLYCOL, 400MM SODIUM IODIDE, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.92 | α = 90 |
b = 78.1 | β = 90 |
c = 86.22 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 300 mm CCD | 2011-03-04 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2011-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.978560 | APS | 21-ID-G |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | |||||||
1,2 | 1.5 | 50 | 98.9 | 0.049 | 0.049 | 22.61 | 7.6 | 70109 | 70109 | -3 | 22.7 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
1,2 | 1.5 | 1.54 | 100 | 0.389 | 0.389 | 4.4 | 5.4 | 5161 |
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 | SAD | THROUGHOUT | STRUCTURE SOLVED VIA IODIDE PHASING AT CUKALPHA, DATA SET 2 WAS USED FOR THIS | 1.5 | 49.92 | 70109 | 69906 | 3526 | 98.7 | 0.134 | 0.134 | 0.133 | 0.15 | RANDOM | 14.71 |
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] | |
-0.19 | 0.62 | -0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.377 |
r_dihedral_angle_4_deg | 17.028 |
r_dihedral_angle_3_deg | 11.658 |
r_dihedral_angle_1_deg | 5.525 |
r_scangle_it | 4.028 |
r_scbond_it | 2.491 |
r_mcangle_it | 1.562 |
r_angle_refined_deg | 1.539 |
r_angle_other_deg | 1.019 |
r_mcbond_it | 0.924 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2031 |
Nucleic Acid Atoms | |
Solvent Atoms | 413 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |