8Q1O
S-layer protein SlpA from Lactobacillus amylovorus, domain I (aa 32-209), important for Self-assembly
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; Condition: 1.0 M Ammonium formate, 0.1 M Sodium acetate pH 5.0, 8 % w/v PGA 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 |
3.24 | 62.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 133.194 | α = 90 |
b = 43.854 | β = 95.498 |
c = 86.384 | 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 | 2019-05-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.004700 | PETRA III, DESY | P11 |
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 | 3.4 | 42.993 | 99.3 | 0.201 | 0.278 | 0.191 | 0.985 | 5.2 | 3.3 | 7031 |
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 | 3.4 | 3.67 | 0.643 | 0.883 | 0.603 | 0.854 | 3.4 |
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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 3.401 | 42.993 | 6996 | 334 | 98.702 | 0.254 | 0.2506 | 0.3306 | 74.477 |
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] | |
-2.589 | -9.292 | 6.019 | -1.612 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 14.328 |
r_dihedral_angle_3_deg | 14.244 |
r_lrange_it | 13.061 |
r_lrange_other | 13.054 |
r_mcangle_other | 9.369 |
r_mcangle_it | 9.368 |
r_dihedral_angle_1_deg | 8.838 |
r_scangle_it | 8.59 |
r_scangle_other | 8.433 |
r_mcbond_it | 5.642 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2676 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
XDS | data reduction |
pointless | data scaling |
PHASER | phasing |