6GHH
Thermodynamic, Crystallographic and Computational Studies of Non Mammalian Fatty Acid Binding to Bovine b-Lactoglobulin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GX9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 293.2 | protein 20 mg/mL, ligand 10mM, 20mM Tris buffer, pH 8, which were mixed with 4 microliter of well solution. Drops were equilibrated against 1 mL of well solution containing 1.43 M sodium citrate and 0.1M Hepes, pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.495 | 50.83 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 53.588 | ¦Á = 90 |
b = 53.588 | ¦Â = 90 |
c = 111.607 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 2 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 | AGILENT ATLAS CCD | 2016-05-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION NOVA | 1.54 |
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 | 1.9 | 13.8 | 99.7 | 8.2 | 4.5 | 17826 |
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 | 1.9 | 2.01 |
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 | 1GX9 | 1.9 | 13.8 | 14552 | 625 | 99.63 | 0.1992 | 0.19709 | 0.24751 | RANDOM | 45.948 |
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] | |
-0.04 | -0.02 | -0.04 | 0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.082 |
r_dihedral_angle_3_deg | 15.532 |
r_dihedral_angle_4_deg | 14.773 |
r_long_range_B_refined | 8.07 |
r_long_range_B_other | 7.994 |
r_dihedral_angle_1_deg | 6.407 |
r_scangle_other | 4.479 |
r_mcangle_it | 4.152 |
r_mcangle_other | 4.15 |
r_scbond_it | 2.777 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1280 |
Nucleic Acid Atoms | |
Solvent Atoms | 76 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALA | data scaling |
MOLREP | phasing |