3OVZ
Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 298 | 0 mM NaAcetate pH=4.0, 0.3 M NaCl, 20% PEG4000, 0.2 M (NH4)2SO4, pH=2.9, 4% Methanol, Cryoprotectant composition:20% PEG4000, 0.1M (NH4)2SO4 pH=2.9, 4% Methanol, 20% PEG 400, pH 5, cocrystallization, hanging drop, temperature 398K | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.02 | 38.61 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 55.741 | α = 90 |
| b = 55.741 | β = 90 |
| c = 128.916 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 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 | IMAGE PLATE | RIGAKU RAXIS IV | 2008-02-12 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | ||
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 | 2.02 | 55.74 | 100 | 14051 | |||||||||||||||
| 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 | 2.02 | 2.09 | 100 | 0.7 | 2 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | In-house cathepsin K structure | 2.02 | 51.16 | 13991 | 698 | 99.7 | 0.247 | 0.244 | 0.308 | 35.26 | ||||||||
| 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] | |
| 0.99 | 0.99 | -1.98 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.592 |
| r_dihedral_angle_3_deg | 18.138 |
| r_dihedral_angle_4_deg | 13.198 |
| r_dihedral_angle_1_deg | 6.198 |
| r_scangle_it | 2.502 |
| r_scbond_it | 1.891 |
| r_angle_refined_deg | 1.785 |
| r_mcangle_it | 1.106 |
| r_angle_other_deg | 1.052 |
| r_mcbond_it | 0.917 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1637 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 79 |
| Heterogen Atoms | 40 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CrystalClear | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| d*TREK | data reduction |
| d*TREK | data scaling |
