4BSK

Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X1XPDB ENTRIES 2X1X, 1FLT AND 2E9W
experimental modelPDB 1FLTPDB ENTRIES 2X1X, 1FLT AND 2E9W
experimental modelPDB 2E9WPDB ENTRIES 2X1X, 1FLT AND 2E9W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9SITTING DROPS AT ROOM TEMPERATURE OVER A RESERVOIR SOLUTION OF 0.1 M BIS-TRIS BUFFER AT PH 8.5-9.5 AND 1.0-1.5 M AMMONIUM SULPHATE.
Crystal Properties
Matthews coefficientSolvent content
5.272

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.66α = 90
b = 166.66β = 90
c = 166.66γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
14.23099.60.0520.99.95765-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
14.24.41001.492.110.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMIRASPDB ENTRIES 2X1X, 1FLT AND 2E9W4.20119.92257215721000.3380.33410.3718135.9
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.257
f_angle_d1.032
f_chiral_restr0.061
f_plane_restr0.006
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1792
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms84

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
autoSHARPphasing
MOLREPphasing
PHENIXrefinement