6WI4
Caspases from Scleractinian Coral
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2J30 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 291 | Protein crystalized in a solution of 0.1 M sodium malonate pH 5.0, 12% w/v polyethylene glycol (PEG) 3350, and conditions were optimized such that the best diffracting crystals of PaCasp7a were obtained at 18 C in a solution of 0.1 M sodium malonate, pH 4.9-5.1, 15-17% PEG 3350 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals for PaCasp7a appeared within 3 to 5 days and were briefly immersed in a cryogenic solution containing 20% PEG 4000, 80% reservoir solution |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.73 | 54.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.416 | α = 90 |
b = 86.848 | β = 90 |
c = 93.666 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER X 16M | 2018-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
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) | 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 | 1.57 | 50 | 98.8 | 0.218 | 0.249 | 0.117 | 9 | 4.9 | 84182 |
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 | 1.57 | 1.6 | 99.5 | 1.461 | 1.642 | 0.733 | 0.255 | 5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | THROUGHOUT | 2J30 | 1.57 | 39.4 | 1.33 | 83910 | 1990 | 98.48 | 0.178 | 0.1772 | 0.209 | 17.6375 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3843 |
Nucleic Acid Atoms | |
Solvent Atoms | 529 |
Heterogen Atoms | 1547 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
PHENIX | phasing |