5X74
The crystal Structure PDE delta in complex with compound (R, R)-1g
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 277 | 0.1 M Sodium acetate, 30 %(v/v) PEG 300 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.96 | 58.41 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 55.7 | α = 90 |
| b = 55.7 | β = 90 |
| c = 114.902 | γ = 120 |
| Symmetry | |
|---|---|
| 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 | AREA DETECTOR | ADSC QUANTUM 315r | 2016-10-31 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.97913 | SSRF | BL17U |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 2.25 | 50 | 99.9 | 0.112 | 0.04 | 24.4 | 9.2 | 10393 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.25 | 2.29 | 100 | 0.208 | 11.93 | 9.4 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 4JV6 | 2.25 | 36.94 | 9805 | 557 | 99.91 | 0.1842 | 0.181 | 0.24119 | RANDOM | 40.307 | ||||||
| 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] | |
| -0.01 | ||||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.746 |
| r_dihedral_angle_4_deg | 19.043 |
| r_dihedral_angle_3_deg | 13.799 |
| r_long_range_B_refined | 8.803 |
| r_long_range_B_other | 8.8 |
| r_scangle_other | 7.101 |
| r_dihedral_angle_1_deg | 6.813 |
| r_scbond_it | 4.723 |
| r_scbond_other | 4.722 |
| r_mcangle_it | 4.316 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1222 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 39 |
| Heterogen Atoms | 44 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
