1YWN

Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPVAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3948.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.953α = 90
b = 95.595β = 90
c = 95.803γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2001-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-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
11.75094.70.04731.386.4337357-3-325.2
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)
11.71.7671.80.3832.634.32767

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1Y6A1.7147.89-335577113995.190.205640.204880.23005RANDOM32.124
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]
0.121.12-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.683
r_dihedral_angle_4_deg16.288
r_dihedral_angle_3_deg12.752
r_dihedral_angle_1_deg5.922
r_scangle_it3.067
r_scbond_it2.214
r_angle_refined_deg1.485
r_mcangle_it1.365
r_mcbond_it1.213
r_angle_other_deg0.823
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.683
r_dihedral_angle_4_deg16.288
r_dihedral_angle_3_deg12.752
r_dihedral_angle_1_deg5.922
r_scangle_it3.067
r_scbond_it2.214
r_angle_refined_deg1.485
r_mcangle_it1.365
r_mcbond_it1.213
r_angle_other_deg0.823
r_symmetry_vdw_refined0.229
r_nbd_refined0.219
r_mcbond_other0.218
r_xyhbond_nbd_refined0.21
r_symmetry_vdw_other0.205
r_nbd_other0.188
r_nbtor_refined0.188
r_symmetry_hbond_refined0.168
r_nbtor_other0.086
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2264
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing