7JL7
Zebrafish Caspase N213T
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5JFT |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | Protein was dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT, concentrated to 4 mg/mL, and inhibitor Ac-DEVD-CHO was added at a 5:1 (w/w) inhibitor/protein ratio. Crystals were obtained at 18 C by the hanging drop vapor diffusion method using a 4 uL drop that contained equal amounts of protein and reservoir solution. Each well contained a reservoir solution (500 uL) of 100 mM sodium citrate, pH 5.4, 23% PEG 6000, 10 mM DTT, and 3 mM NaN3. Flat, sheet-like crystals appeared within 14 days, and we used microseeding to obtain diffraction-quality crystals. In this case, crystal trays were set up as described above and incubated for 24 hours. The flat sheet crystals were collected and treated with seed beads using a kit from Hampton Research. A 4 uL drop containing flat sheet crystals was added to a tube containing seed beads. Reservoir solution (10 uL) was pipetted on the cover slide to remove all crystals from the coverslip, and the procedure was repeated five times. The resulting mixture of crystals and seed beads was vortexed for 30 seconds and cooled on ice for 10 seconds, and the procedure was repeated six times. Serial dilutions of the treated crystals were set up from 10-1 to 10-3, and 0.5 uL of the 10-2 dilution crystal seeds was added into the drops of the 24-hour crystal tray. Larger cube-shaped crystals appeared within 14 days. The crystals were collected and frozen in liquid nitrogen following the addition of 20% MPD plus the reservoir solution. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.13 | 42.35 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 56.305 | α = 90 |
b = 74.58 | β = 90 |
c = 133.413 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2018-08-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0 | APS | 22-BM |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.05 | 35.91 | 90.51 | 0.843 | 30.77 | 5.1 | 32428 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.07 | 2.11 | 0.069 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 5JFT | 2.05 | 35.91 | 1.33 | 32428 | 2000 | 90.51 | 0.2051 | 0.2018 | 0.2533 | 37.4882 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
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 | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3717 |
Nucleic Acid Atoms | |
Solvent Atoms | 109 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |