3OT3
X-ray crystal structure of compound 22k bound to human Chk1 kinase domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BRM | PDB ENTRY 2BRM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 296 | 0.1M Tris-Cl pH 7.5, 25% v/v Glycerol, 2.5% v/v DMSO, 1% v/v 1-butanol, 4 to 10% v/v PEG 3.25K, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.83 | α = 90 |
b = 65.78 | β = 94.41 |
c = 57.72 | 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 | 200 | CCD | MAR CCD 165 mm | 2006-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-BM | 1.0 | APS | 17-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (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 | 1.44 | 57.5 | 90.5 | 0.054 | 0.053 | 19.5 | 2.9 | 59517 | 53853 | 18.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.44 | 1.48 | 90.1 | 0.433 | 0.367 | 2.4 | 2.8 | 2652 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 2BRM | 1.44 | 57 | 59517 | 53853 | 2692 | 0.185 | 0.185 | 0.185 | 0.202 | EXTENDED from 2BRM, RANDOM |
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 |
t_dihedral_angle_d | 17.115 |
t_improper_torsion | 4.367 |
t_it | 1.43 |
t_angle_deg | 0.91 |
t_nbd | 0.016 |
t_gen_planes | 0.014 |
t_bond_d | 0.01 |
t_trig_c_planes | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2103 |
Nucleic Acid Atoms | |
Solvent Atoms | 277 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
BUSTER | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
BUSTER | phasing |