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Structure of the G6 Fab, a phage derived Fab fragment, in complex with VEGF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FLT Search model for VEGF was based on 1FLT, search model for the Fab was based on 2FJF. experimental model PDB 2FJF Search model for VEGF was based on 1FLT, search model for the Fab was based on 2FJF.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 2.0 M Ammonium sulfate, 5% Isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.64 66.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.88 α = 90 b = 117.88 β = 90 c = 212.562 γ = 120
Symmetry Space Group P 31 2 1
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 2003-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97946 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 99.7 42803 42763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.7
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 Search model for VEGF was based on 1FLT, search model for the Fab was based on 2FJF. 2.8 20 40510 40389 2152 99.73 0.21 0.20077 0.1987 0.2014 0.23916 0.2376 RANDOM 36.61
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] -1.16 -0.58 -1.16 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.797 r_scangle_it 5.615 r_mcangle_it 4.841 r_scbond_it 3.594 r_mcbond_it 3.112 r_angle_refined_deg 1.55 r_angle_other_deg 0.859 r_symmetry_hbond_refined 0.304 r_nbd_other 0.236 r_nbd_refined 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.797 r_scangle_it 5.615 r_mcangle_it 4.841 r_scbond_it 3.594 r_mcbond_it 3.112 r_angle_refined_deg 1.55 r_angle_other_deg 0.859 r_symmetry_hbond_refined 0.304 r_nbd_other 0.236 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.196 r_symmetry_vdw_other 0.166 r_symmetry_vdw_refined 0.137 r_nbtor_other 0.091 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002 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_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 Atoms Number Protein Atoms 8031 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing