4CL7
Crystal structure of VEGFR-1 domain 2 in presence of Cobalt
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FLT | PDB ENTRY 1FLT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | CRYSTAL WERE OBTAINED BY HANGING DROP METHOD FROM 1MM VEGFR1-D2, 5MM HEPES/NAOH PH7.0, 10MM COCL2, 100 MM BIS-TRIS/HCL PH6.5 15%(W/V) PEG3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 27.746 | α = 87.05 |
b = 41.711 | β = 82.25 |
c = 94.694 | γ = 73.03 |
Symmetry | |
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Space Group | P 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 | CCD | ADSC CCD | KIRKPATRICK-BAEZ MIRRORSWITH PT COATING | 2009-11-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 |
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 | 2 | 19.47 | 97.1 | 0.07 | 10.74 | 1.8 | 26362 | 2 | 17.48 |
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 | 2.07 | 96.6 | 0.33 | 3.01 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1FLT | 2 | 19.469 | 1.97 | 26358 | 1294 | 97.05 | 0.1707 | 0.1675 | 0.2332 | 17.58 |
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] | |
-0.2689 | 0.3828 | -0.1891 | 0.2025 | -0.0657 | 0.0664 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.826 |
f_angle_d | 0.983 |
f_chiral_restr | 0.063 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3020 |
Nucleic Acid Atoms | |
Solvent Atoms | 281 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |