5YSB
Crystal structure of beta-1,2-glucooligosaccharide binding protein in ligand-free form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3UOR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | 0.15M zinc acetate, 15% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.925 | α = 90 |
b = 74.925 | β = 90 |
c = 120.844 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 270 | 2015-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0000 | Photon Factory | AR-NW12A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 2.2 | 50 | 98.8 | 0.097 | 0.047 | 21 | 5.5 | 38141 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.2 | 2.24 | 100 | 0.571 | 0.263 | 0.906 | 5.7 |
Refinement
Statistics | |||||||||||||||||||
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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 | 3UOR | 2.2 | 19.24 | 36488 | 1856 | 99.57 | 0.19246 | 0.18975 | 0.24679 | RANDOM | 49.947 |
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] | |
0.23 | 0.12 | 0.23 | -0.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.729 |
r_dihedral_angle_4_deg | 17.808 |
r_dihedral_angle_3_deg | 16.025 |
r_long_range_B_refined | 7.677 |
r_long_range_B_other | 7.677 |
r_dihedral_angle_1_deg | 6.2 |
r_scangle_other | 5.203 |
r_mcangle_other | 3.986 |
r_mcangle_it | 3.985 |
r_scbond_it | 3.435 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6093 |
Nucleic Acid Atoms | |
Solvent Atoms | 205 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data processing |
MOLREP | phasing |
PHENIX | phasing |