6U2A
ShyA endopeptidase from Vibrio cholera (open form)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GUI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 295 | Protein (0.5 microliter): 18 mg/ml in 20 mM Tris-HCl, 150 mM NaCl pH 7.6 Precipitant (0.5 microliter): 0.25 M sodium citrate, 10% polyethylene glycol 3350, 0.1 M Tris-HCl pH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 59.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.272 | α = 90 |
b = 82.492 | β = 102.692 |
c = 82.522 | 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 | 125 | PIXEL | DECTRIS EIGER X 9M | 2018-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.07811 | APS | 21-ID-D |
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 | 2.025 | 54.9 | 54.1 | 0.055 | 0.059 | 0.011 | 0.998 | 9.8 | 7 | 17391 | 60.31 |
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 | 2.026 | 2.276 | 66.7 | 1.13 | 1.234 | 0.487 | 0.549 | 1.6 | 6.2 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2GUI | 2.3 | 36.58 | 16347 | 842 | 74.4 | 0.2538 | 0.2936 | Random | 78.09 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.736 |
f_angle_d | 0.635 |
f_chiral_restr | 0.0473 |
f_bond_d | 0.0034 |
f_plane_restr | 0.0033 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2852 |
Nucleic Acid Atoms | |
Solvent Atoms | 10 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHASER | phasing |
PDB_EXTRACT | data extraction |
STARANISO | data scaling |
autoPROC | data scaling |
XDS | data reduction |