7QLE
Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I (aa 32-198)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition A5 (0.2 M Magnesium formate dihydrate, 20 % w/v PEG 3350) with protein end concentration of 7.5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 130.127 | α = 90 |
b = 39.036 | β = 101.662 |
c = 60.058 | 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 | PIXEL | DECTRIS PILATUS 6M-F | 2015-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.97895 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.6 | 48.37 | 99.3 | 0.143 | 0.198 | 0.137 | 0.986 | 7.1 | 3.3 | 9254 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.6 | 2.72 | 0.574 | 0.794 | 0.547 | 0.666 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7QLD | 2.6 | 48.367 | 9252 | 462 | 99.111 | 0.203 | 0.2003 | 0.2583 | 32.184 |
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] | |
2.068 | -0.156 | 1.597 | -3.318 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.648 |
r_dihedral_angle_3_deg | 15.089 |
r_lrange_it | 8.224 |
r_lrange_other | 8.223 |
r_dihedral_angle_1_deg | 7.237 |
r_mcangle_it | 4.836 |
r_mcangle_other | 4.834 |
r_scangle_it | 4.497 |
r_scangle_other | 4.496 |
r_mcbond_it | 2.906 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2193 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |