4COG
Crystal structure of kynurenine formamidase from Burkholderia cenocepacia
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 293 | 14 % (W/V) PEG 3350, 5 MM COCL2, 5 MM CDCL2, 5 MM MGCL2 AND 5 MM NICL2. 293 K. | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.26 | 45.57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 76.859 | α = 90 |
| b = 50.12 | β = 94.15 |
| c = 135.197 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 | MIRRORS | 2012-09-23 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 | |
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 | 1.6 | 28.37 | 99.3 | 0.07 | 12.8 | 3.6 | 134904 | ||||||||||||
| 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 | 1.6 | 1.69 | 99.8 | 0.48 | 3 | 3.6 | |||||||||||||
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 | KYNURENINE FORMAMIDASE FROM PSEUDOMONAS AERUGINOSA | 1.6 | 134.84 | 128111 | 6778 | 99.21 | 0.15063 | 0.14886 | 0.18431 | RANDOM | 18.874 | ||||||
| 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] | |
| -0.19 | -0.04 | 0.28 | -0.08 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.829 |
| r_dihedral_angle_4_deg | 18.843 |
| r_dihedral_angle_3_deg | 12.653 |
| r_dihedral_angle_1_deg | 6.21 |
| r_scangle_it | 3.639 |
| r_mcangle_it | 2.684 |
| r_scbond_it | 2.601 |
| r_angle_refined_deg | 2.422 |
| r_mcbond_it | 1.834 |
| r_metal_ion_refined | 0.537 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6212 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1068 |
| Heterogen Atoms | 131 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
