6VKO
Crystal Structure of human PARP-1 CAT domain bound to inhibitor UKTT15
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5DS3 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 2M Ammonium Sulfate, Bis-Tris pH6.5 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.61 | 52.82 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 139.701 | α = 90 |
| b = 129.751 | β = 111.36 |
| c = 102.72 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 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 | PIXEL | DECTRIS PILATUS3 S 6M | 2018-12-21 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.1158 | ALS | 8.3.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | 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 | 2.8 | 95.664 | 95.4 | 0.152 | 0.17 | 0.076 | 5.3 | 4.6 | 39944 | 39944 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.8 | 2.95 | 95.5 | 0.709 | 0.709 | 0.799 | 0.359 | 1.1 | 4.5 | ||||||||||
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 | 5ds3 | 2.8 | 20 | 37777 | 2021 | 94.69 | 0.2857 | 0.2843 | 0.3122 | RANDOM | 90.658 | ||||||
| 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] | |
| 1.51 | 2.05 | -2.25 | -0.67 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.44 |
| r_dihedral_angle_3_deg | 20.359 |
| r_dihedral_angle_4_deg | 16.876 |
| r_dihedral_angle_1_deg | 8.746 |
| r_angle_refined_deg | 1.471 |
| r_angle_other_deg | 1.091 |
| r_chiral_restr | 0.057 |
| r_bond_refined_d | 0.006 |
| r_gen_planes_refined | 0.005 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10712 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 31 |
| Heterogen Atoms | 204 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOSFLM | data reduction |
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
