7QFJ
Crystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain II (aa 194-362)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293.15 | Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Midas screen condition 50 (0.1M Tris, 50% v/v Pentaerythritol propoxylate (5/4 PO/OH)) with protein end concentration of 5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop, co-crystallization with 0.1 ul 2mM HgCl2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 59.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.679 | α = 90 |
b = 143.016 | β = 96.699 |
c = 73.441 | 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 PILATUS 6M | 2020-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 11.2C | 0.94290 | ELETTRA | 11.2C |
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 | 2.5 | 48.63 | 99.9 | 0.084 | 0.1 | 0.053 | 0.998 | 17.1 | 6.8 | 46501 |
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 | 2.5 | 2.59 | 0.6 | 0.715 | 0.384 | 0.866 | 6.7 |
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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | RoseTTAfold ab initio prediction | 2.5 | 46.028 | 46471 | 2290 | 99.927 | 0.207 | 0.2056 | 0.2425 | RANDOM | 47.942 |
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] | |
-4.037 | 0.827 | 3.417 | 0.415 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.171 |
r_dihedral_angle_3_deg | 14.395 |
r_dihedral_angle_4_deg | 11.204 |
r_lrange_it | 9.706 |
r_scangle_it | 7.354 |
r_mcangle_it | 6.578 |
r_dihedral_angle_1_deg | 6.48 |
r_scbond_it | 5.063 |
r_mcbond_it | 4.336 |
r_angle_refined_deg | 1.336 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7788 |
Nucleic Acid Atoms | |
Solvent Atoms | 216 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |