3QNW
Caspase-6 in complex with Z-VAD-FMK inhibitor
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 4.3 | 298 | 0.1 M lithium sulfate, 0.1 M sodium citrate, 11% 2-propanol , VAPOR DIFFUSION, temperature 298K, pH 4.3 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.2 | 44.06 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 87.206 | α = 90 |
| b = 65.446 | β = 91.24 |
| c = 91.718 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 315 | 2010-01-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9763 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.65 | 29.1 | 99.2 | 0.114 | 14.8 | 7.5 | 30244 | 30002 | |||||||||||
| 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 | 2.65 | 2.79 | 98.8 | 0.564 | 3.6 | 7.6 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 entry 2wdp | 2.65 | 29.1 | 28824 | 28380 | 1505 | 98.46 | 0.24275 | 0.24038 | 0.28713 | RANDOM | 24.792 | |||||
| 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] | |
| 1.31 | -0.02 | -2.25 | 0.93 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.767 |
| r_dihedral_angle_4_deg | 17.694 |
| r_dihedral_angle_3_deg | 13.3 |
| r_dihedral_angle_1_deg | 5.004 |
| r_scangle_it | 0.857 |
| r_angle_refined_deg | 0.815 |
| r_angle_other_deg | 0.746 |
| r_mcangle_it | 0.657 |
| r_scbond_it | 0.528 |
| r_mcbond_it | 0.353 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6898 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 80 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| GDA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
