5DVI
High resolution crystal Structure of glucose complexed periplasmic glucose binding protein (ppGBP) from P. putida CSV86
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 295 | 0.1 M phosphate citrate buffer, 2 M ammonium sulphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.94 | α = 90 |
b = 119.05 | β = 90 |
c = 66.6 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | MARMOSAIC 225 mm CCD | 2014-07-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.9763 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.25 | 44.39 | 99.7 | 16.41 | 6.24 | 224933 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.25 | 1.35 | 99.2 | 2.71 | 5.47 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.25 | 40.76 | 213608 | 11245 | 99.68 | 0.12339 | 0.1219 | 0.15153 | RANDOM | 23.264 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.95 | -0.89 | -0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 35.352 |
r_dihedral_angle_2_deg | 34.255 |
r_dihedral_angle_4_deg | 22.164 |
r_sphericity_bonded | 17.349 |
r_dihedral_angle_3_deg | 11.744 |
r_dihedral_angle_1_deg | 5.667 |
r_long_range_B_refined | 5.464 |
r_long_range_B_other | 4.757 |
r_scangle_other | 4.228 |
r_scbond_it | 3.603 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5952 |
Nucleic Acid Atoms | |
Solvent Atoms | 981 |
Heterogen Atoms | 87 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |