4MH6
2.8 Angstrom Crystal Structure of Type III Secretion Protein YscO from Vibrio parahaemolyticus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.2 | 295 | Protein: 2.28 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: JCSG+ (C9), 0.1M Sodium/Potasium phosphate pH 6.2, 25% (v/v) 1,2 Propanediol, 10% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.13 | 70.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 149.114 | α = 90 |
b = 149.114 | β = 90 |
c = 63.422 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 2 |
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 | 2013-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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 | 2.8 | 30 | 99.9 | 0.139 | 18.3 | 9.6 | 9084 | 9084 | -3 | 55.3 |
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 | 2.8 | 2.85 | 100 | 0.603 | 4.2 | 10 | 436 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.8 | 29.24 | 8645 | 8645 | 434 | 99.69 | 0.19195 | 0.18946 | 0.24308 | RANDOM | 52.031 |
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] | |
0.46 | 0.46 | -0.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 24.165 |
r_dihedral_angle_4_deg | 13.841 |
r_dihedral_angle_3_deg | 11.605 |
r_long_range_B_refined | 8.74 |
r_long_range_B_other | 8.69 |
r_scangle_other | 5.917 |
r_mcangle_it | 4.262 |
r_mcangle_other | 4.26 |
r_scbond_it | 3.759 |
r_scbond_other | 3.553 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1347 |
Nucleic Acid Atoms | |
Solvent Atoms | 93 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
SHELXS | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |