4OW3
Thermolysin structure determined by free-electron laser
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2TLI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 6.5 | 298 | 300 ul of the protein stock was mixed in a 1:1 ratio with 40% PEG 2000, 100 mM MES pH 6.5, 5 mM CaCl2. Crystallization occurred within minutes. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.8933 | α = 90 |
b = 92.8933 | β = 90 |
c = 130.438 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 | 298 | PIXEL | CS-PAD detector | 2011-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.269, 1.297 | SLAC LCLS | CXI |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.1 | 68.5 | 99.1 | 50.2 | 209 | 19861 | 14.3263474589 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.1 | 2.18 | 91.2 | 5.6 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2TLI | 2.1 | 68.4723333423 | 1.44173097843 | 19861 | 1042 | 99.0326601845 | 0.219654161884 | 0.217242670815 | 0.263168484633 | 16.2875323051 |
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 | 12.8953940052 |
f_angle_d | 0.682438849813 |
f_chiral_restr | 0.025759577597 |
f_bond_d | 0.00289852909819 |
f_plane_restr | 0.00240657682604 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2404 |
Nucleic Acid Atoms | |
Solvent Atoms | 338 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |