1BJ1

VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VPFPDB ENTRY 2VPF AND 1FVD
experimental modelPDB 1FVDPDB ENTRY 2VPF AND 1FVD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.666

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.86α = 90
b = 66.98β = 94.27
c = 140.51γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM1996-03-12M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

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
12.420960.0718.63.863147
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)
2.42.4881.30.1283.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VPF AND 1FVD2.4860401590894.80.1960.1960.266THIN RESOLUTION SHELLS42
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]
3.7-0.31-8.54.8
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d27.97
x_scangle_it7.3
x_scbond_it5
x_mcangle_it4.1
x_mcbond_it2.6
x_angle_deg1.66
x_improper_angle_d1.47
x_bond_d0.012
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d27.97
x_scangle_it7.3
x_scbond_it5
x_mcangle_it4.1
x_mcbond_it2.6
x_angle_deg1.66
x_improper_angle_d1.47
x_bond_d0.012
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 Atoms8136
Nucleic Acid Atoms
Solvent Atoms548
Heterogen Atoms10

Software

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