3WZD

KDR in complex with ligand lenvatinib


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION9.52770.1M CHES,5-20% PEG 8000, pH 9.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4549.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.334α = 90
b = 84.225β = 100.2
c = 46.892γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00003SLSX06SA

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
11.5746.1599.50.064.244907
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)
11.571.8299.70.4444.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.5746.1540823408299.520.183720.180890.21188RANDOM29.321
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]
0.11-1.17-0.510.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.617
r_dihedral_angle_4_deg19.719
r_dihedral_angle_3_deg11.547
r_dihedral_angle_1_deg5.942
r_scbond_it4.204
r_mcangle_it3.31
r_mcbond_it2.584
r_mcbond_other2.583
r_angle_refined_deg1.58
r_angle_other_deg1.027
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.617
r_dihedral_angle_4_deg19.719
r_dihedral_angle_3_deg11.547
r_dihedral_angle_1_deg5.942
r_scbond_it4.204
r_mcangle_it3.31
r_mcbond_it2.584
r_mcbond_other2.583
r_angle_refined_deg1.58
r_angle_other_deg1.027
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms2224
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling