2PGO
The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh) from Azoarcus sp. strain 22Lin
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 60% MPD, 0.02M sodium acetate, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.17 | 43.41 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 123.6 | α = 90 |
| b = 123.6 | β = 90 |
| c = 144.3 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 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 QUANTUM 4 | 2003-12-09 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | M | MAD | ||||||||||
| 3 | 1 | x-ray | M | SINGLE WAVELENGTH | ||||||||||
| 4 | 1 | x-ray | M | SINGLE WAVELENGTH | ||||||||||
| 1,2,3,4 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.939 | ESRF | ID14-4 |
| 2 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 1.0052, 1.0093, 1.023 | ESRF | ID14-4 |
| 3 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 1.005 | ESRF | ID14-4 |
| 4 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 1.072 | ESRF | ID14-4 |
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 | ||||||||
| 1,2,3,4 | 1.2 | 40 | 77 | 0.063 | 12 | 2.48 | 259345 | ||||||||||||
| 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) | |||||||||||
| 1,2,3,4 | 1.2 | 1.3 | 14 | 0.115 | 5.1 | 1.1 | 20256 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MAD, MIRAS | THROUGHOUT | 1.26 | 5 | 259345 | 259345 | 13524 | 93.24 | 0.09782 | 0.09782 | 0.09669 | 0.11963 | RANDOM | 8.189 | |||||
| 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] | |
| -0.04 | -0.04 | 0.09 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.987 |
| r_dihedral_angle_4_deg | 15.226 |
| r_dihedral_angle_3_deg | 13.543 |
| r_dihedral_angle_1_deg | 6.733 |
| r_sphericity_free | 5.033 |
| r_sphericity_bonded | 4.494 |
| r_scangle_it | 3.907 |
| r_scbond_it | 3.086 |
| r_mcangle_it | 2.356 |
| r_angle_refined_deg | 2.014 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8886 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1212 |
| Heterogen Atoms | 183 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| ADSC | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SHARP | phasing |
