3ITN
Crystal structure of Pseudo-activated Procaspase-3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291.15 | Proteins were dialyzed in a buffer of 10 mM Tris-HCl (pH 8.5) and 1 mM DTT. The protein was concentrated to 10 mg/mL using Amicon ultrafree centrifugal filter devices, and inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl (pH 8.5), concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl (pH 8.5), 10 mM DTT, and 3 mM NaN3. Crystals were obtained by the hanging drop vapor diffusion method. Concentrated protein (2 L) was mixed 1:1 with a reservoir solution that contained 100 mM sodium citrate (pH 5), 3 mM NaN3, 10 mM DTT, and 17% PEG 6000 (w/v). The crystallization plates were incubated at 18 C., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.224 | α = 90 |
b = 84.607 | β = 90 |
c = 96.171 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | 100 | CCD | MARMOSAIC 300 mm CCD | 2006-10-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.00 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (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 | 1.63 | 33.79 | 91.79 | 0.52 | 0.444 | 5.45 | 35601 | 32677 | 3 | 3 |
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) | ||||||||||||
1.63 | 99 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | Caspase-3 PDB code 2J30 | 1.63 | 33.79 | 1 | 35601 | 30659 | 3063 | 0.22 | 0.1987 | 0.1987 | 0.2242 | Randomly selected 10% of reflections |
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 |
c_angle_d | 1.26877 |
c_bond_d | 0.004748 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1963 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |