7WIK
Crystal structure of oligoribonuclease of Mycobacterium smegmatis mc2 155
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.4 | 298 | 0.1M Tris-HCl, pH8.4, 0.2M Lithium sulphate, 30% v/v PEG-4000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.32 | 46.97 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 60.25 | α = 90 |
| b = 97.26 | β = 90 |
| c = 146.73 | 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 | 80 | PIXEL | PSI JUNGFRAU 4M | 2018-05-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.96863 | ESRF | ID29 |
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 | 1.87 | 81.07 | 99.5 | 0.056 | 0.07 | 0.032 | 0.999 | 13.5 | 4.6 | 71290 | |||||||||
| 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 | 1.874 | 1.906 | 99.8 | 0.694 | 0.794 | 0.377 | 0.803 | 2 | 4.3 | ||||||||||
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 | 2igi | 1.87 | 81.07 | 67736 | 3553 | 99.46 | 0.1813 | 0.1792 | 0.2224 | RANDOM | 33.637 | ||||||
| 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] | |
| 3.74 | -1.03 | -2.71 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.865 |
| r_dihedral_angle_4_deg | 16.302 |
| r_dihedral_angle_3_deg | 13.068 |
| r_dihedral_angle_1_deg | 6.154 |
| r_angle_refined_deg | 1.461 |
| r_angle_other_deg | 1.353 |
| r_chiral_restr | 0.072 |
| r_bond_refined_d | 0.009 |
| r_gen_planes_refined | 0.007 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6137 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 647 |
| Heterogen Atoms | 154 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| autoPROC | data reduction |
| PHASER | phasing |
