Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with ADP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.5 | 10-14% PEG 8000, 20% GLYCEROL, 0.1 M MES/NAOH PH 6.5, 200 MM CACL2 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.92 | 57.9 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 68.664 | α = 90 |
| b = 68.664 | β = 90 |
| c = 147.006 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 |
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 PIXEL | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 | |
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 | 2.08 | 46.22 | 99.7 | 0.1 | 11.2 | 5.6 | 46431 | 2 | |||||||||||
| 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 | 2.08 | 2.19 | 100 | 0.44 | 3.8 | 5.5 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.08 | 37.82 | 43014 | 3370 | 99.65 | 0.16102 | 0.15884 | 0.16 | 0.18869 | 0.19 | RANDOM | 52.161 | |||||
| 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] | |
| -15.26 | -15.26 | 30.53 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.566 |
| r_dihedral_angle_3_deg | 14.335 |
| r_dihedral_angle_4_deg | 11.274 |
| r_dihedral_angle_1_deg | 6.665 |
| r_mcangle_it | 2.3 |
| r_scbond_it | 1.627 |
| r_angle_refined_deg | 1.584 |
| r_mcbond_it | 1.487 |
| r_mcbond_other | 1.487 |
| r_angle_other_deg | 0.891 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4309 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 295 |
| Heterogen Atoms | 148 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
