Crystal structure of the putative periplasmic solute-binding protein from Campylobacter jejuni
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 25% P3350, 0.1M B-Tris pH 6.5, MgSulphate 1mM |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.1 | 41.54 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 82.19 | α = 68.88 |
| b = 89.276 | β = 82.52 |
| c = 100.394 | γ = 70.66 |
| 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 | MARMOSAIC 300 mm CCD | beryllium lenses | 2016-04-14 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97857 | APS | 21-ID-G |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2 | 30 | 98.1 | 0.11 | 0.9 | 21.8 | 11.8 | 167225 | |||||||||||
| 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 | 2.03 | 97 | 0.69 | 3.7 | 11.5 | |||||||||||||
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 | SAD | THROUGHOUT | 2 | 30 | 155567 | 8289 | 95.81 | 0.17815 | 0.17571 | 0.18 | 0.22393 | 0.23 | RANDOM | 30.194 | |||||
| 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] | |
| -0.17 | 0.2 | -0.19 | 0.36 | -0.13 | -0.18 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.267 |
| r_dihedral_angle_4_deg | 15.183 |
| r_dihedral_angle_3_deg | 10.553 |
| r_long_range_B_refined | 5.07 |
| r_long_range_B_other | 5.07 |
| r_dihedral_angle_1_deg | 2.933 |
| r_angle_refined_deg | 1.73 |
| r_scangle_other | 1.646 |
| r_mcangle_it | 1.405 |
| r_mcangle_other | 1.405 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 20409 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1619 |
| Heterogen Atoms | 115 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data scaling |
| PHENIX | phasing |
| PHENIX | model building |
