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Structure of the B20-4 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 Fab was based on 2FJF. experimental model PDB 2FJF Search model for VEGF was based on 1FLT, search model for Fab was based on 2FJF.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 292 0.1 M Sodium acetate, 1.6 M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 5.046684 75.627563
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.538 α = 90 b = 165.538 β = 90 c = 150.548 γ = 120
Symmetry Space Group P 31 1 2
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 2004-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
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 3.1 50 99.8 42840 42755
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 3.1 3.21 100
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-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 Fab was based on 2FJF. 3.1 30 42910 39869 2120 97.99 0.21 0.20038 0.19829 0.2394 0.2634 RANDOM 55.043
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] 2.32 1.16 2.32 -3.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.786 r_scangle_it 6.163 r_mcangle_it 5.716 r_scbond_it 3.787 r_mcbond_it 3.34 r_angle_refined_deg 1.42 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.786 r_scangle_it 6.163 r_mcangle_it 5.716 r_scbond_it 3.787 r_mcbond_it 3.34 r_angle_refined_deg 1.42 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 8103 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing