2XVX
Cobalt chelatase CbiK (periplasmatic) from Desulvobrio vulgaris Hildenborough (Native)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.5 | CRYSTALLIZATION SOLUTION: 100MM TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS MADE BY ADDING 1UL OF PROTEIN PLUS 2UL OF CRYSTALLIZATION SOLUTION. | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.6 | 66.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 121.062 | α = 90 |
| b = 121.062 | β = 90 |
| c = 120.246 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 4 2 2 |
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 | 2007-04-20 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 | |
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 | 42.8 | 99.9 | 0.08 | 7.6 | 28 | 35365 | 25.5 | |||||||||||
| 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 | 99.2 | 0.83 | 0.9 | 20.3 | |||||||||||||
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 | MODEL OBTAINED WITH THE PROTEIN CO- CRYSTALLIZED WITH COBALT. | 1.9 | 85.6 | 33596 | 1768 | 99.86 | 0.17477 | 0.17351 | 0.19875 | RANDOM | 29.552 | ||||||
| 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] | |
| -0.3 | -0.3 | 0.6 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.235 |
| r_dihedral_angle_4_deg | 19.06 |
| r_dihedral_angle_3_deg | 13.18 |
| r_dihedral_angle_1_deg | 5.154 |
| r_scangle_it | 4.967 |
| r_scbond_it | 3.044 |
| r_mcangle_it | 2.075 |
| r_angle_refined_deg | 1.767 |
| r_mcbond_it | 1.145 |
| r_chiral_restr | 0.122 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1979 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 217 |
| Heterogen Atoms | 133 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
