1DEU
CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN X: A CYSTEINE PROTEASE WITH THE PROREGION COVALENTLY LINKED TO THE ACTIVE SITE CYSTEINE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1HUC | Cathepsin B (PDB code 1HUC), Reference: Musil et al EMBO.J 1991, 10, 2321-2330 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 292 | 300 mM (NH4)2SO4, 12% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.82 | α = 90 |
b = 84.82 | β = 90 |
c = 169.72 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 | ADSC QUANTUM | 1999-02-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X8C | NSLS | X8C |
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 | 1.7 | 45 | 95.4 | 0.048 | 19.5 | 3.5 | 521645 | 82047 | 0.3 | 16.4 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.7 | 1.78 | 90.7 | 0.208 | 1.5 | 7673 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Cathepsin B (PDB code 1HUC), Reference: Musil et al EMBO.J 1991, 10, 2321-2330 | 1.7 | 45 | 1 | 2 | 82047 | 74610 | 1849 | 95.1 | 0.204 | 0.215 | RANDOM | 20.7 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
c_angle_d | 24.7 |
c_dihedral_angle_d | 24.2 |
c_angle_deg | 2.5 |
c_scangle_it | 1.08 |
c_mcangle_it | 0.98 |
c_improper_angle_d | 0.71 |
c_scbond_it | 0.67 |
c_mcbond_it | 0.55 |
c_bond_d | 0.034 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4193 |
Nucleic Acid Atoms | |
Solvent Atoms | 428 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Adxv | data processing |
SCALEPACK | data scaling |
AMoRE | phasing |
CNS | refinement |