4ASE

CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH TIVOZANIB (AV-951)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ASDPDB ENTRY 4ASD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2286CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION METHOD AT 13 DEGREES C BY THE USING PRECIPITANT SOLUTIONS CONTAINING APPROXIMATELY: 0.2M SODIUM CITRATE AND 14-21% (W/V) POLYETHYLENE GLYCOL 3350., pH 6.2
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.095α = 90
b = 56.299β = 96.33
c = 51.991γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray85PIXELDECTRIS PILATUS 6M2011-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

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
11.8343.299.10.0317.43.333988126.2
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)
11.831.9399.80.42.53.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4ASD1.8343.3233984102298.70.2070.2070.231RANDOM42.3
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]
12.32-3.28-9.74-2.58
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.8
c_angle_deg0.8
c_improper_angle_d0.59
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.8
c_angle_deg0.8
c_improper_angle_d0.59
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2455
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms32

Software

Software
Software NamePurpose
CNSrefinement
autoPROCdata reduction
SCALAdata scaling
CNXphasing