3C7Q

Structure of VEGFR2 kinase domain in complex with BIBF1120


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VR2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42770.1M HEPES, 2.1M Ammonium Sulphate, 3% PEG MME 550, 10mM Beta-Mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3848.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.25α = 90
b = 94.44β = 90
c = 96.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9799SLSX06SA

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
123098.40.0879.9123933-332.839
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)
122.191.20.5592

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1VR22.128.54199341993410501000.2210.2170.279RANDOM24.366
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]
-0.872.84-1.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.284
r_dihedral_angle_4_deg17.038
r_dihedral_angle_3_deg16.389
r_dihedral_angle_1_deg8.311
r_scangle_it2.529
r_scbond_it1.789
r_angle_refined_deg1.633
r_mcangle_it1.354
r_mcbond_it1.184
r_angle_other_deg0.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.284
r_dihedral_angle_4_deg17.038
r_dihedral_angle_3_deg16.389
r_dihedral_angle_1_deg8.311
r_scangle_it2.529
r_scbond_it1.789
r_angle_refined_deg1.633
r_mcangle_it1.354
r_mcbond_it1.184
r_angle_other_deg0.997
r_symmetry_hbond_refined0.267
r_symmetry_vdw_other0.22
r_nbd_refined0.206
r_nbd_other0.2
r_symmetry_vdw_refined0.197
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.181
r_mcbond_other0.155
r_chiral_restr0.114
r_nbtor_other0.089
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2362
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms65

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction