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Crystal Structure of the Fab YADS2 Complexed with h-VEGF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPF The VEGF is from pdb entry 1VPF. The Fab is from an in-house determined structure.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 292 LITHIUM CHLORIDE, PEG 6000, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.2 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.504 α = 90 b = 149.588 β = 90 c = 117.421 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2003-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.000 SSRL BL9-2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 50 97.3 0.076 0.076 18.7 4.8 21429 20861 -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) Redundancy Number Unique Reflections (All) 1 2.8 2.9 82.92 0.4 0.4 2.5 83.2 2110
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT The VEGF is from pdb entry 1VPF. The Fab is from an in-house determined structure. 2.8 20 21229 19702 1023 97.63 0.2197 0.2197 0.21786 0.2196 0.25447 0.2586 RANDOM 46.845
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] -8.87 1.62 7.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.592 r_mcangle_it 5.231 r_scangle_it 4.696 r_mcbond_it 3.211 r_scbond_it 2.869 r_angle_refined_deg 1.334 r_angle_other_deg 0.945 r_symmetry_vdw_refined 0.342 r_nbd_other 0.224 r_symmetry_vdw_other 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.592 r_mcangle_it 5.231 r_scangle_it 4.696 r_mcbond_it 3.211 r_scbond_it 2.869 r_angle_refined_deg 1.334 r_angle_other_deg 0.945 r_symmetry_vdw_refined 0.342 r_nbd_other 0.224 r_symmetry_vdw_other 0.208 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.134 r_nbtor_other 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 4077 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing