5NV9
Substrate-bound outward-open state of a Na+-coupled sialic acid symporter reveals a novel Na+-site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 0.1M sodium citrate pH 5, 0.2-0.5M potassium chloride, 30-40% pentaerythritol propoxylate (5/4/PO/OH) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.19 | 61.48 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 130.59 | ¦Á = 90 |
b = 98.07 | ¦Â = 92.15 |
c = 54.78 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 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 | PIXEL | DECTRIS PILATUS3 S 6M | 2015-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.97858 | Diamond | I24 |
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 | 1.95 | 78.4 | 99.2 | 6.43 | 3.24 | 49833 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | THROUGHOUT | 1.95 | 78.4 | 47316 | 2536 | 99.22 | 0.20104 | 0.19882 | 0.24346 | RANDOM | 29.973 |
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] | |
2.91 | 0.17 | -1.27 | -1.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.932 |
r_dihedral_angle_4_deg | 15.148 |
r_dihedral_angle_3_deg | 14.169 |
r_long_range_B_refined | 6.322 |
r_long_range_B_other | 6.131 |
r_dihedral_angle_1_deg | 5.626 |
r_scangle_other | 4.268 |
r_scbond_it | 2.995 |
r_scbond_other | 2.954 |
r_mcangle_other | 2.935 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3707 |
Nucleic Acid Atoms | |
Solvent Atoms | 220 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
SHELXS | phasing |