8AOL
Crystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain III (aa 363-499)
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 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Wizard 1/2 screen condition 66 (20 % w/v PEG 3000, 200 mM Ca(OAc)2, 100 mM Tris base/HCl pH 7.0) with protein end concentration of 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 |
5.3 | 76.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 133.174 | α = 90 |
b = 133.174 | β = 90 |
c = 70.572 | γ = 120 |
Symmetry | |
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Space Group | P 62 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 | PIXEL | DECTRIS PILATUS 6M | 2018-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.0332 | 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 | 2.4 | 48.432 | 100 | 0.198 | 0.209 | 0.065 | 0.997 | 10.1 | 19.1 | 14935 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.4 | 2.49 | 1.516 | 1.596 | 0.496 | 0.844 | 19.4 |
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 | 8ALU | 2.4 | 48.432 | 14914 | 766 | 99.966 | 0.179 | 0.1779 | 0.205 | 46.79 |
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] | |
-3.069 | -1.534 | -3.069 | 9.955 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.375 |
r_lrange_it | 16.475 |
r_lrange_other | 16.469 |
r_dihedral_angle_4_deg | 14.794 |
r_dihedral_angle_3_deg | 14.677 |
r_scangle_it | 13.869 |
r_scangle_other | 13.862 |
r_scbond_it | 11.134 |
r_scbond_other | 11.125 |
r_dihedral_angle_1_deg | 8.658 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1143 |
Nucleic Acid Atoms | |
Solvent Atoms | 143 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |