1FLT

VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VPF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.44α = 90
b = 71.13β = 105.28
c = 77.86γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray160CCDADSC QUANTUM1997-02-01M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.730990.0528.374704723.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7695.80.273.53

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 REPLACEMENT/NCS AVERAGINGTHROUGHOUT1VPF1.7200.245678227596.80.1980.1980.261RANDOM31.9
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]
1.905-2.748-4.03862.1336
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d28.8
x_scangle_it6.3
x_mcangle_it4.9
x_scbond_it3.9
x_mcbond_it2.4
x_angle_deg1.76
x_improper_angle_d0.99
x_bond_d0.013
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d28.8
x_scangle_it6.3
x_mcangle_it4.9
x_scbond_it3.9
x_mcbond_it2.4
x_angle_deg1.76
x_improper_angle_d0.99
x_bond_d0.013
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3090
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing