1TZI

Crystal Structure of the Fab YADS2 Complexed with h-VEGF


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.1292LITHIUM CHLORIDE, PEG 6000, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.261.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.504α = 90
b = 149.588β = 90
c = 117.421γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.000SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.85097.30.0760.07618.74.82142920861-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.982.920.40.42.583.22110

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 REPLACEMENTTHROUGHOUTThe VEGF is from pdb entry 1VPF. The Fab is from an in-house determined structure.2.8202122919702102397.630.21970.21970.217860.25447RANDOM46.845
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]
-8.871.627.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.592
r_mcangle_it5.231
r_scangle_it4.696
r_mcbond_it3.211
r_scbond_it2.869
r_angle_refined_deg1.334
r_angle_other_deg0.945
r_symmetry_vdw_refined0.342
r_nbd_other0.224
r_symmetry_vdw_other0.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.592
r_mcangle_it5.231
r_scangle_it4.696
r_mcbond_it3.211
r_scbond_it2.869
r_angle_refined_deg1.334
r_angle_other_deg0.945
r_symmetry_vdw_refined0.342
r_nbd_other0.224
r_symmetry_vdw_other0.208
r_nbd_refined0.203
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.134
r_nbtor_other0.086
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4077
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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