5XAT
Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277 | 100 mM MES pH 6.0-6.5, 100-200 mM NaCl, 32-36% PEG400 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.79 | 67.53 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 87.668 | α = 86.1 |
| b = 91.874 | β = 82.22 |
| c = 96.32 | γ = 69.66 |
| 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 | MAR CCD 130 mm | 2016-11-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.979 | PAL/PLS | 7A (6B, 6C1) |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.76 | 95.41 | 99.2 | 21.2 | 1.9 | 26874 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 3.8 | 3.9 | 98.6 | 1.9 | |||||||||||||||
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 | 5A1S | 3.76 | 95.41 | 25473 | 1401 | 94.95 | 0.26908 | 0.26748 | 0.29815 | RANDOM | 238.985 | ||||||
| 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] | |
| -14.59 | 4.45 | -4.59 | 2.51 | -2.87 | 13.15 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 34.492 |
| r_long_range_B_other | 34.492 |
| r_dihedral_angle_2_deg | 32.026 |
| r_mcangle_it | 22.106 |
| r_mcangle_other | 22.104 |
| r_scangle_other | 20.252 |
| r_dihedral_angle_3_deg | 13.869 |
| r_mcbond_other | 13.817 |
| r_mcbond_it | 13.816 |
| r_dihedral_angle_4_deg | 13.205 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 12271 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 4 |
| Heterogen Atoms | 62 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
