8T9B
Structure of the CK variant of Fab F1 (FabC-F1) in complex with the C-terminal FN3 domain of EphA2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8T7F | Fab (heavy and light chain) |
in silico model | Modeller | SwissModel model of residues 438-528 of human EphA2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 1.5 M sodium formate, 100 mM Tris-HCl, pH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.86 | 74.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.661 | α = 90 |
b = 130.65 | β = 89.76 |
c = 222.996 | γ = 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 EIGER X 16M | Mirrors | 2021-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.97918 | APS | 24-ID-E |
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 | 4.2 | 131.33 | 97.3 | 0.173 | 0.211 | 0.119 | 0.997 | 4.2 | 3 | 31847 | 101.35 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 4.2 | 4.43 | 97.8 | 1.185 | 0.813 | 0.602 | 1.2 | 3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 8T7F | 4.2 | 66.12 | 1.34 | 31108 | 1713 | 96.25 | 0.2968 | 0.2957 | 0.315 | 156.28 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.0788 |
f_angle_d | 1.0062 |
f_chiral_restr | 0.0568 |
f_plane_restr | 0.0202 |
f_bond_d | 0.0049 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15657 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |