4Y01
Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9 | 293 | BICINE pH 9.0, sodium chloride, PEG MME 550 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.6 | 52.7 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 99.788 | α = 90 |
| b = 115.486 | β = 90 |
| c = 147.57 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 95 | CCD | ADSC QUANTUM 270 | 2012-12-20 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.98 | Photon Factory | BL-17A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.46 | 40 | 99.6 | 0.11 | 12.6 | 6.6 | 62234 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 2.46 | 2.52 | 99.5 | 2.1 | 3.1 | ||||||||||||||
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 | MAD | THROUGHOUT | 2.46 | 40 | 58784 | 2980 | 99.19 | 0.1866 | 0.18415 | 0.23339 | RANDOM | 41.04 | |||||||
| 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] | |
| -0.57 | 2.1 | -1.53 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.207 |
| r_dihedral_angle_4_deg | 19.514 |
| r_dihedral_angle_3_deg | 18.495 |
| r_long_range_B_other | 7.408 |
| r_long_range_B_refined | 7.407 |
| r_dihedral_angle_1_deg | 7.079 |
| r_scangle_other | 5.706 |
| r_mcangle_it | 4.471 |
| r_mcangle_other | 4.471 |
| r_scbond_it | 3.6 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11216 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 186 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| xia2 | data processing |
| SHARP | phasing |
| ARP | model building |
