8SOU
Proteinase K Multiconformer Model at 363K
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3Q5G |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | Proteinase K was dissolved at pH 7.5 to 30 mg/mL in a 50 mM TRIS buffer . The protein was crystallized using a hanging drop setup on a 24 well VDX plate with sealant and 22 mm thick siliconized circle cover slides by mixing equal amounts of protein solution with ammonium sulfate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.458 | α = 90 |
b = 68.458 | β = 90 |
c = 104.967 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | 363 | PIXEL | DECTRIS EIGER X 16M | 2019-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 1.12709 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.54 | 35.58 | 96.51 | 0.999 | 6.54 | 2 | 37357 | 17.95 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.542 | 1.597 | 81.34 | 0.383 | 0.79 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FREE R-VALUE | 1.54 | 35.58 | 1.34 | 36238 | 1999 | 96.53 | 0.1756 | 0.1728 | 0.2233 | 21.52 |
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 | 11.4009 |
f_angle_d | 0.5092 |
f_chiral_restr | 0.0427 |
f_plane_restr | 0.0041 |
f_bond_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2070 |
Nucleic Acid Atoms | |
Solvent Atoms | 93 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |