5KXA
Selective Inhibition of Autotaxin is Effective in Mouse Models of Liver Fibrosis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ZGA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 20% PEG 3350, 0.1 M Sodium Acetate pH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.1 | α = 71.56 |
b = 55.506 | β = 79.75 |
c = 70.075 | γ = 81.09 |
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 | 133 | CCD | RAYONIX MX-325 | 2015-03-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 1.00 | APS | 21-ID-G |
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 | 2.59 | 65.84 | 98.4 | 7.1 | 1.1 | 23660 |
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 | 4ZGA | 2.59 | 65.84 | 19537 | 1052 | 85.88 | 0.17719 | 0.17328 | 0.24733 | RANDOM | 53.771 |
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] | |
-0.33 | -1.1 | 1.25 | -1.49 | 0.25 | 1.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.226 |
r_dihedral_angle_3_deg | 17.215 |
r_dihedral_angle_4_deg | 15.118 |
r_dihedral_angle_1_deg | 7.521 |
r_long_range_B_refined | 6.423 |
r_long_range_B_other | 6.423 |
r_scangle_other | 4.864 |
r_mcangle_it | 4.855 |
r_mcangle_other | 4.855 |
r_scbond_it | 3.403 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5893 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |