2XIR
Crystal structure of the VEGFR2 kinase domain in complex with PF- 00337210 (N,2-dimethyl-6-(7-(2-morpholinoethoxy)quinolin-4-yloxy) benzofuran-3-carboxamide)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 286 | PROTEIN PRODUCTION, PROTEIN PURIFICATION, AND COCRYSTALLIZATION WERE PERFORMED AS PREVIOUSLY DESCRIBED (PUBLISHED INTERNATIONAL PATENT APPLICATION WO 2004/092217 HANGING DROP VAPOR DIFFUSION AT 13 DEGREES C. 2 MICROLITERS OF A 7.7 MG/ML PROTEIN SOLUTION (IN 50 MM HEPES 7.5, 30 MM SODIUM CHLORIDE, 5 MM DTT, AND 5% DMSO) WAS MIXED WITH 2 MICROLITERS OF CRYSTALLIZATION SOLUTION (100 MM HEPES PH 7.5, 20% PEG 6K AND 5% MPD) AND SUSPENDED OVER 1 ML OF CRYSTALLIZATION SOLUTION PLUS 5 MICROLITERS BME. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 135.267 | α = 90 |
b = 56.827 | β = 94.18 |
c = 52.187 | 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 | 89 | CCD | ADSC CCD | 2004-08-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | ALS | 5.0.2 |
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 | 1.45 | 50 | 95.8 | 0.06 | 22 | 4.4 | 67226 | 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 | 1.45 | 1.5 | 68.2 | 0.48 | 1.22 | 2.3 |
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 1VR2 | 1.5 | 19.92 | 59334 | 3178 | 98.83 | 0.21852 | 0.21747 | 0.23808 | RANDOM | 23.671 |
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] | |
0.16 | -0.63 | -0.41 | 0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.431 |
r_angle_other_deg | 16.781 |
r_dihedral_angle_4_deg | 16.03 |
r_dihedral_angle_3_deg | 13.856 |
r_dihedral_angle_1_deg | 4.921 |
r_scangle_it | 1.636 |
r_angle_refined_deg | 1.091 |
r_scbond_it | 1.017 |
r_mcangle_it | 0.77 |
r_mcbond_it | 0.449 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2338 |
Nucleic Acid Atoms | |
Solvent Atoms | 337 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |