4P6E
Crystal Structure of Human Cathepsin S Bound to a Non-covalent Inhibitor
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | EVAPORATION | 4.6 | 295 | 21% PEG 8000, 150 mM ammonium sulfate, 100 mM sodium acetate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.71 | 54.63 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 85.692 | α = 90 |
| b = 85.692 | β = 90 |
| c = 151.496 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 2 2 |
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 | MAR CCD 165 mm | 2008-03-17 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.979 | APS | 31-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 28.07 | 99.5 | 7 | 7.3 | 53044 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 1.8 | 28.07 | 50867 | 1022 | 97.78 | 0.17616 | 0.1757 | 0.19914 | RANDOM | 29.166 | ||||||||
| 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] | |
| -0.36 | -0.36 | 0.72 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.446 |
| r_dihedral_angle_3_deg | 11.621 |
| r_dihedral_angle_4_deg | 10.182 |
| r_dihedral_angle_1_deg | 5.358 |
| r_long_range_B_refined | 5.263 |
| r_long_range_B_other | 4.87 |
| r_scangle_other | 3.404 |
| r_scbond_other | 2.209 |
| r_scbond_it | 2.19 |
| r_mcangle_it | 2.02 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3381 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 417 |
| Heterogen Atoms | 63 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
