3ZBX
X-ray Structure of c-Met kinase in complex with inhibitor 6-((6-(4- fluorophenyl)-(1,2,4)triazolo(4,3-b)(1,2,4)triazin-3-yl)methyl) quinoline.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WGJ | PDB ENTRY 2WGJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.2 | 286 | C-MET COCRYSTALS WERE OBTAINED AT 13 DEGREES C BY THE HANGING DROP VAPOR DIFFUSION METHOD BY MIXING 1.2 MICROLITERS OF PROTEIN SOLUTION (CONTAINING 7-13 MG/ML C-MET KD (RESIDUES 1051-1348) WITH A 5 FOLD MOLAR EXCESS OF C-MET INHIBITOR COMPOUND) WITH 1.2 MICROLITERS OF SOLUTION CONTAINING (0.05M CITRATE-PHOSPHATE PH 4.2, 200M NACL, AND 17.4% POLYETHYLENE GLYCOL MW=3350) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.857 | α = 90 |
b = 94.127 | β = 90 |
c = 46.418 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 96 | CCD | ADSC CCD | 2005-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.2 | 50 | 84.9 | 0.07 | 13.1 | 2.8 | 15108 | 12.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.28 | 81.2 | 0.28 | 3.5 | 2.8 |
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 | PDB ENTRY 2WGJ | 2.2 | 47.06 | 14207 | 429 | 80.2 | 0.179 | 0.179 | 0.237 | RANDOM | 24.6 |
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] | |
-2.23 | -7.89 | 10.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 19.6 |
c_scangle_it | 3.14 |
c_scbond_it | 2.23 |
c_mcangle_it | 1.95 |
c_mcbond_it | 1.26 |
c_angle_deg | 0.8 |
c_improper_angle_d | 0.59 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2256 |
Nucleic Acid Atoms | |
Solvent Atoms | 278 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CCP4 | phasing |