9ETF
Crystal structure of recombinant chicken liver Bile Acid Binding Protein (cL-BABP) in complex with lithocholic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7O0K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 281 | 25% wt/vol PEG-3500, 200 mM lithium sulfate monohydrate, and 100 mM BIS-TRIS, pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 49.97 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 36.627 | ¦Á = 90 |
b = 61.156 | ¦Â = 96.09 |
c = 64.037 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS EIGER2 X 16M | 2022-05-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97949 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 63.67 | 96.4 | 0.056 | 0.068 | 0.037 | 0.998 | 10.4 | 3 | 13885 | 34.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.2 | 2.32 | 98.4 | 0.437 | 0.532 | 0.299 | 0.856 | 2.2 |
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 | 2.2 | 36.45 | 13273 | 607 | 96.29 | 0.21194 | 0.20855 | 0.27767 | RANDOM | 47.7 |
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] | |
-0.01 | 0.01 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.784 |
r_dihedral_angle_3_deg | 18.092 |
r_dihedral_angle_4_deg | 13.729 |
r_long_range_B_refined | 10.655 |
r_dihedral_angle_1_deg | 7.899 |
r_mcangle_it | 6.249 |
r_scbond_it | 5.332 |
r_mcbond_it | 4.31 |
r_angle_refined_deg | 1.578 |
r_chiral_restr | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1863 |
Nucleic Acid Atoms | |
Solvent Atoms | 140 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |