6VAH
Crystal structure of human TEAD2 transcription factor in complex with Flufenamic acid derivative
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5DQ8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 3.5M Na Formate, and 0.1M Bis-Tris Propane pH7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.792 | α = 90 |
b = 61.307 | β = 118.1 |
c = 79.862 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | PIXEL | DECTRIS EIGER X 16M | 2019-11-14 | 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) | 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 | 2.1 | 50 | 97 | 0.093 | 0.105 | 0.048 | 9.2 | 4.1 | 28671 |
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 | 2.1 | 2.14 | 88.2 | 0.551 | 0.645 | 0.326 | 0.847 | 2.9 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 5DQ8 | 2.11 | 39.07 | 27256 | 1415 | 96.33 | 0.2055 | 0.2035 | 0.2425 | RANDOM | 50.628 |
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] | |
4.52 | 2.02 | -0.98 | -3.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.141 |
r_dihedral_angle_3_deg | 16.505 |
r_dihedral_angle_4_deg | 15.942 |
r_dihedral_angle_1_deg | 8.46 |
r_angle_refined_deg | 1.383 |
r_angle_other_deg | 1.209 |
r_chiral_restr | 0.056 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3133 |
Nucleic Acid Atoms | |
Solvent Atoms | 28 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |