3DH4
Crystal Structure of Sodium/Sugar symporter with bound Galactose from vibrio parahaemolyticus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 278 | 100 mM Hepes, 200mM Ca Acetate, 20-25% PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.37 | 71.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.28 | α = 109.7 |
b = 109.21 | β = 92.02 |
c = 127.58 | γ = 102.11 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2008-02-25 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | CCD | MARMOSAIC 300 mm CCD | 2008-02-17 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 0.97930 | ALS | 5.0.2 |
2 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97930 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.7 | 30 | 91.3 | 0.113 | 8.6 | 4 | 103009 |
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 | 2.7 | 2.8 | 69.9 | 0.429 | 1.55 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
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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 | SIRAS | THROUGHOUT | 2.7 | 30 | 57175 | 2998 | 53.33 | 0.27063 | 0.26979 | 0.28715 | RANDOM | 37.531 |
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] | |
0.35 | 0.26 | -0.61 | 0.19 | 0.06 | -0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.834 |
r_dihedral_angle_3_deg | 19.479 |
r_dihedral_angle_4_deg | 17.133 |
r_dihedral_angle_1_deg | 6.796 |
r_angle_other_deg | 4.379 |
r_scangle_it | 2.467 |
r_scbond_it | 2.303 |
r_mcangle_it | 1.819 |
r_angle_refined_deg | 1.071 |
r_mcbond_it | 0.949 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15416 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |