1YWN

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y6Apdb entry 1Y6A

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