4L7C
Structure of keap1 kelch domain with 2-{[(1S)-2-{[(1R,2S)-2-(1H-tetrazol-5-yl)cyclohexyl]carbonyl}-1,2,3,4-tetrahydroisoquinolin-1-yl]methyl}-1H-isoindole-1,3(2H)-dione
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZGK | PDB ENTRY 1ZGK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 296 | 1 ul of protein at 12 mg/ml in 20 mM Tris-HCl pH 7.5, 5 mM DTT, 5 mM compound 1 + 2 ul of 2.15 M Sodium Acetate , VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.21 | 61.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.29 | α = 90 |
b = 125.61 | β = 90 |
c = 132.63 | γ = 90 |
Symmetry | |
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Space Group | P 21 2 21 |
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 PILATUS 2M | mirror | 2012-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1 | SLS | X06DA |
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 | 2.4 | 36.71 | 99.92 | 50637 | 48009 | 2 | 2 |
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 | 2.4 | 2.462 | 100 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1ZGK | 2.4 | 36.66 | 50637 | 48009 | 2573 | 99.92 | 0.26626 | 0.26626 | 0.26547 | 0.28064 | RANDOM | 42.493 |
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] | |
0.76 | 0.06 | -0.81 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.935 |
r_dihedral_angle_4_deg | 14.905 |
r_dihedral_angle_3_deg | 13.628 |
r_dihedral_angle_1_deg | 5.286 |
r_angle_refined_deg | 0.956 |
r_angle_other_deg | 0.643 |
r_chiral_restr | 0.051 |
r_bond_refined_d | 0.004 |
r_gen_planes_refined | 0.002 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6609 |
Nucleic Acid Atoms | |
Solvent Atoms | 199 |
Heterogen Atoms | 125 |
Software
Software | |
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Software Name | Purpose |
GO.COM | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |