5R5E
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13848a
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.02 | 39 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 49.62 | ¦Á = 90 |
| b = 52.28 | ¦Â = 90 |
| c = 101.69 | ¦Ã = 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2016-07-02 | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92819 | Diamond | I04-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.58 | 44.59 | 100 | 0.075 | 0.082 | 0.032 | 0.999 | 12.4 | 6.4 | 37057 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.58 | 1.62 | 100 | 1.724 | 1.87 | 0.717 | 0.538 | 6.6 | 2669 | ||||||||||
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 | FOURIER SYNTHESIS | THROUGHOUT | 5LF9 | 1.58 | 44.63 | 35009 | 1989 | 99.9 | 0.1909 | 0.1888 | 0.2245 | RANDOM | 26.243 | ||||||
| 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] | |
| 1.99 | -2.18 | 0.19 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.107 |
| r_dihedral_angle_4_deg | 17.5 |
| r_dihedral_angle_3_deg | 12.854 |
| r_dihedral_angle_1_deg | 6.868 |
| r_mcangle_it | 2.789 |
| r_mcbond_it | 2.019 |
| r_mcbond_other | 2.001 |
| r_angle_refined_deg | 1.584 |
| r_angle_other_deg | 1.373 |
| r_chiral_restr | 0.078 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2198 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 161 |
| Heterogen Atoms | 30 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| REFMAC | phasing |
