6AYS
Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with hexylthio-DADMe-Immucillin-A
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4WKN | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 295 | 100 mM Bis-Tris pH 5.5, 200 mM Magnesium Chloride, 25% (w/v) PEG 3350 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.1 | 40.29 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 67.367 | α = 87.54 |
| b = 75.288 | β = 89.05 |
| c = 90.437 | γ = 71.13 |
| Symmetry | |
|---|---|
| Space Group | P 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 | CCD | RAYONIX MX-225 | 2017-03-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97931 | APS | 31-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.7 | 90.35 | 97.3 | 0.99 | 8.1 | 4.2 | 179940 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.7 | 1.73 | 95.7 | 0.84 | 2.1 | 4.3 | |||||||||||||
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 | 4WKN | 1.7 | 90.35 | 171111 | 8797 | 97.33 | 0.23119 | 0.23033 | 0.24786 | RANDOM | 23.148 | ||||||
| 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] | |
| -0.32 | -0.64 | 0.06 | 0.19 | 0.07 | -0.33 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.144 |
| r_dihedral_angle_4_deg | 23.054 |
| r_dihedral_angle_3_deg | 13.647 |
| r_dihedral_angle_1_deg | 6.253 |
| r_long_range_B_refined | 4.375 |
| r_long_range_B_other | 4.375 |
| r_scangle_other | 2.103 |
| r_mcangle_it | 1.796 |
| r_mcangle_other | 1.796 |
| r_angle_refined_deg | 1.334 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 14049 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1710 |
| Heterogen Atoms | 220 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
