2JH3
The crystal structure of DR2241 from Deinococcus radiodurans at 1.9 A resolution reveals a multi-domain protein with structural similarity to chelatases but also with two additional novel domains
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.8 | 17-20% PEG3350 AND 0.15-0.20 M MGCL2., pH 8.80 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.5 | 51 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 124.78 | α = 90 |
| b = 128.69 | β = 90 |
| c = 135.08 | 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 | 100 | CCD | ADSC CCD | MIRRORS | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.9 | 20 | 98.8 | 0.08 | 9.3 | 3.2 | 168727 | 22.06 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.9 | 2 | 98.6 | 0.62 | 1.9 | 3.2 | |||||||||||||
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 | SIRAS | THROUGHOUT | 1.9 | 20 | 165141 | 3400 | 98.7 | 0.19 | 0.189 | 0.238 | RANDOM | 31.69 | |||||||
| 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] | |
| -1.22 | 0.69 | 0.53 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.928 |
| r_dihedral_angle_4_deg | 20.797 |
| r_dihedral_angle_3_deg | 16.343 |
| r_dihedral_angle_1_deg | 6.676 |
| r_scangle_it | 3.868 |
| r_scbond_it | 2.656 |
| r_angle_refined_deg | 1.841 |
| r_mcangle_it | 1.775 |
| r_mcbond_it | 1.488 |
| r_angle_other_deg | 0.993 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 13982 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 984 |
| Heterogen Atoms | 32 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| XDS | data scaling |
| SHARP | phasing |
| SOLVE | phasing |
| REFMAC | refinement |
