2FJF

Structure of the G6 Fab, a phage derived VEGF binding Fab


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.729225% PEG 3350, 0.1 M Sodium Acetate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.1961.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 274.919α = 90
b = 192.229β = 117
c = 154.108γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
12.65501000.063.9205393205298
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)
12.652.741000.52

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.6520205393200469447699.850.20.199760.198560.24835SHELLS11.368
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]
-1.1-1.840.99-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.272
r_scangle_it2.701
r_mcangle_it2.359
r_scbond_it1.923
r_mcbond_it1.538
r_angle_refined_deg1.213
r_nbd_refined0.203
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.123
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.272
r_scangle_it2.701
r_mcangle_it2.359
r_scbond_it1.923
r_mcbond_it1.538
r_angle_refined_deg1.213
r_nbd_refined0.203
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.123
r_chiral_restr0.077
r_symmetry_hbond_refined0.049
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms39000
Nucleic Acid Atoms
Solvent Atoms642
Heterogen Atoms

Software

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