2XV7
Crystal structure of vascular endothelial growth factor D
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2X1W | VEGF-C FROM PDB ENTRY 2X1W |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.2 | A SINGLE VEGF-D CRYSTAL GREW IN 6 WEEKS AT ROOM TEMPERATURE OVER A RESERVOIR SOLUTION OF 0.1 M PHOSPHATE/CITRATE BUFFER AT PH 4.2, 40 % ETHANOL (V/V), 5 % PEG 1000 (W/V). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.72 | α = 90 |
b = 95.72 | β = 90 |
c = 70.94 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2010-05-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | SLS | X06SA |
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 | 2.9 | 80 | 99.7 | 0.09 | 18 | 8.8 | 36742 | 67.19 |
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 | 2.9 | 3.05 | 99.7 | 0.77 | 3.8 | 9.2 |
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 | VEGF-C FROM PDB ENTRY 2X1W | 2.9 | 19.893 | 1.99 | 4543 | 454 | 99.71 | 0.2626 | 0.2548 | 0.3325 | 81.3 |
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] | |
2.8326 | 2.8326 | -5.6651 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 33.883 |
f_angle_d | 1.543 |
f_chiral_restr | 0.089 |
f_plane_restr | 0.011 |
f_bond_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 774 |
Nucleic Acid Atoms | |
Solvent Atoms | 13 |
Heterogen Atoms | 100 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |