Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (AMP, ADP and sulfate complex)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291 | Berkeley H5: 100 mM MgCl2, 100 mM Li2SO4, 25% PEG 400. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP but hydrolyzed AMP and ADP were observed. plate 20560 A12 drop 1, Puck: PSL-1103, Cryo: 20% PEG 200 + 80% crystallant |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.82 | 56.42 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 66.424 | α = 90 |
| b = 169.4 | β = 90 |
| c = 170.618 | 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 | PIXEL | DECTRIS EIGER2 XE 9M | 2025-12-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.9786 | NSLS-II | 19-ID |
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 | 2.49 | 50.07 | 100 | 0.162 | 0.169 | 0.046 | 0.998 | 13.9 | 13.3 | 68380 | |||||||||
| 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 | 2.49 | 2.55 | 100 | 1.855 | 1.928 | 0.521 | 0.724 | 13.5 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.49 | 50.07 | 1.33 | 68291 | 3298 | 99.96 | 0.199 | 0.1963 | 0.1986 | 0.2495 | 0.2477 | ||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 11.688 |
| f_angle_d | 0.808 |
| f_chiral_restr | 0.049 |
| f_plane_restr | 0.008 |
| f_bond_d | 0.006 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11387 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 68 |
| Heterogen Atoms | 242 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
