7QFI
Crystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain I (aa 31-182)
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; SG+ screen condition 50 (25 % 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 |
1.83 | 32.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.35 | α = 90 |
b = 38.347 | β = 93.927 |
c = 82.745 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 PILATUS3 2M | 2018-10-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.87313 | ESRF | ID23-2 |
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 | 1.5 | 41.28 | 99.1 | 0.073 | 0.101 | 0.069 | 0.995 | 7.7 | 3.2 | 37359 |
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 | 1.5 | 1.53 | 0.479 | 0.653 | 0.441 | 0.755 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | AB INITIO PHASING | FREE R-VALUE | 1.5 | 41.28 | 37340 | 1877 | 98.914 | 0.188 | 0.1868 | 0.2224 | 19.25 |
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] | |
1.353 | -0.57 | 1.006 | -2.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.448 |
r_dihedral_angle_4_deg | 31.783 |
r_dihedral_angle_3_deg | 11.99 |
r_dihedral_angle_1_deg | 7.545 |
r_lrange_it | 6.574 |
r_lrange_other | 6.481 |
r_scangle_it | 4.767 |
r_scangle_other | 4.766 |
r_scbond_it | 3.095 |
r_scbond_other | 3.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1949 |
Nucleic Acid Atoms | |
Solvent Atoms | 232 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
Arcimboldo | phasing |
ARP/wARP | model building |