4ASD

Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with SORAFENIB (BAY 43-9006)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2286CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION METHOD AT 13 DEGREES C 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 = 135.818α = 90
b = 56.479β = 95.42
c = 52.052γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray81IMAGE PLATEMARRESEARCHMIRRORS2007-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2000

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
12.025092.20.04383.7239081
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)
12.022.0943.60.1361.9

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 4AG82.0315226311218940.178310.175470.23022RANDOM29.658
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]
0.84-0.37-0.44-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.999
r_dihedral_angle_4_deg21.002
r_dihedral_angle_3_deg17.192
r_dihedral_angle_1_deg5.747
r_scangle_it3.102
r_scbond_it2.003
r_mcangle_it1.365
r_angle_refined_deg1.303
r_mcbond_it0.799
r_angle_other_deg0.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.999
r_dihedral_angle_4_deg21.002
r_dihedral_angle_3_deg17.192
r_dihedral_angle_1_deg5.747
r_scangle_it3.102
r_scbond_it2.003
r_mcangle_it1.365
r_angle_refined_deg1.303
r_mcbond_it0.799
r_angle_other_deg0.694
r_nbd_other0.375
r_nbtor_refined0.307
r_symmetry_vdw_refined0.249
r_xyhbond_nbd_refined0.238
r_nbtor_other0.225
r_nbd_refined0.195
r_symmetry_hbond_refined0.185
r_mcbond_other0.161
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2453
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CCP4phasing