1RWX
Crystal structure of human caspase-1 in complex with 4-oxo-3-{6-[4-(quinoxalin-2-yloxy)-benzoylamino]-2-thiophen-2-yl-hexanoylamino}-butyric acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RWN | PDB ID 1RWN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 278 | 0.1M PIPES, 88mM (NH4)2SO4, 25% PEG 2000 MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.371 | α = 90 |
b = 63.371 | β = 90 |
c = 162.399 | 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 | 180 | IMAGE PLATE | RIGAKU RAXIS IV | 2003-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.85 | 20 | 98.6 | 0.08 | 29162 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.85 | 1.91 | 95.9 | 0.38 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ID 1RWN | 1.85 | 20 | 29162 | 27113 | 1445 | 97.93 | 0.21564 | 0.21428 | 0.24197 | RANDOM | 23.925 |
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] | |
0.68 | 0.68 | -1.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.002 |
r_scangle_it | 2.306 |
r_mcangle_it | 2.289 |
r_scbond_it | 1.421 |
r_mcbond_it | 1.307 |
r_angle_refined_deg | 0.868 |
r_nbd_refined | 0.159 |
r_symmetry_vdw_refined | 0.108 |
r_symmetry_hbond_refined | 0.094 |
r_xyhbond_nbd_refined | 0.074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2102 |
Nucleic Acid Atoms | |
Solvent Atoms | 249 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data reduction |
d*TREK | data scaling |
AMoRE | phasing |