9G7P
Crystal structure of Shewanella putrefaciens PE-like toxin, Spx
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IKQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 294.15 | 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000 (condition C10 of the PACT premier Screen, Molecular Dimensions) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.196 | α = 90 |
b = 121.196 | β = 90 |
c = 125.216 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 EIGER2 XE 16M | 2021-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 1.79 | 104.83 | 100 | 0.28 | 0.287 | 0.062 | 0.997 | 7.5 | 21.5 | 193517 |
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 | 1.79 | 1.82 | 99.7 | 3.695 | 3.784 | 0.811 | 0.339 | 0.4 | 21.2 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.861 | 104.83 | 172116 | 8476 | 99.694 | 0.187 | 0.185 | 0.1837 | 0.2204 | 0.2202 | 34.028 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
0.486 | 0.243 | 0.486 | -1.576 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.939 |
r_dihedral_angle_4_deg | 15.838 |
r_dihedral_angle_3_deg | 11.536 |
r_dihedral_angle_1_deg | 6.731 |
r_lrange_it | 5.49 |
r_lrange_other | 5.44 |
r_scangle_it | 3.686 |
r_scangle_other | 3.686 |
r_mcangle_it | 2.876 |
r_mcangle_other | 2.876 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13905 |
Nucleic Acid Atoms | |
Solvent Atoms | 1241 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |