X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FLTSearch model for VEGF was based on 1FLT, search model for Fab was based on 2FJF.
experimental modelPDB 2FJFSearch model for VEGF was based on 1FLT, search model for Fab was based on 2FJF.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62920.1 M Sodium acetate, 1.6 M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
5.04668475.627563

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.538α = 90
b = 165.538β = 90
c = 150.548γ = 120
Symmetry
Space GroupP 31 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.0ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.15099.84284042755
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.21100

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSearch model for VEGF was based on 1FLT, search model for Fab was based on 2FJF.3.1304291039869212097.990.210.200380.198290.2394RANDOM55.043
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]
2.321.162.32-3.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.786
r_scangle_it6.163
r_mcangle_it5.716
r_scbond_it3.787
r_mcbond_it3.34
r_angle_refined_deg1.42
r_symmetry_vdw_refined0.237
r_nbd_refined0.223
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.786
r_scangle_it6.163
r_mcangle_it5.716
r_scbond_it3.787
r_mcbond_it3.34
r_angle_refined_deg1.42
r_symmetry_vdw_refined0.237
r_nbd_refined0.223
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.116
r_chiral_restr0.098
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8103
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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