1PAU
Crystal structure of the complex of apopain with the tetrapeptide aldehyde inhibitor AC-DEVD-CHO
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ICE | PROTEIN COMPONENT OF INTERLEUKIN-1BETA CONVERTING ENZYME (PDB ENTRY 1ICE) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF PROTEIN:INHIBITOR SOLUTION (8.7 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.5, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7% PEG-6000 (W/W), 0.10 MOLAR SODIUM CITRATE PH 5.0, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE, vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.81 | α = 90 |
b = 84.62 | β = 90 |
c = 96.79 | 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 | 293 | AREA DETECTOR | SIEMENS | 1995-11-09 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
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 | 2.5 | 36 | 87.1 | 0.0634 | 0.0555 | 17.4 | 2.33 | 8929 | 31.34 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.5 | 2.59 | 87.1 | 0.257 | 0.262 | 2.59 | 2.27 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE-R | PROTEIN COMPONENT OF INTERLEUKIN-1BETA CONVERTING ENZYME (PDB ENTRY 1ICE) | 2.5 | 20 | 2 | 7987 | 845 | 78 | 0.195 | 0.195 | 0.275 | RANDOM | 23.56 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 24.14 |
x_angle_deg | 1.308 |
x_improper_angle_d | 1.091 |
x_bond_d | 0.007 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1905 |
Nucleic Acid Atoms | |
Solvent Atoms | 34 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
SAINT | data reduction |
SAINT | data scaling |
X-PLOR | phasing |