☰ Navigation Tabs
Crystal structure of a bispecific DutaFab in complex with human VEGF121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJ1 1BJ1, 1JPS experimental model PDB 1JPS 1BJ1, 1JPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 VEGFA-121 from Peprotech, catalogue number 100-20A, was mixed at a 1:1 molar ratio to VEGF monomer. The complex was concentrated to 11 mg/ml. Crystallization involved hanging drop vapour diffusion against 0.1 M MES pH 6.5 and 1.6 M magnesium sulphate. Crystals grew in about 120 days and were frozen in liquid nitrogen with 20 % glycerol as cryoprotectant.
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.08 α = 90 b = 107.875 β = 95.34 c = 87.369 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD KB MIRRORS 2014-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.9 30 98.9 0.212 6.7 3 28318 37.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.1 98.2 0.842 1.5 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BJ1, 1JPS 2.905 29.294 28317 1416 98.879 0.216 0.2124 0.2801 0.2385 35.023
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] -1.396 -0.886 0.703 0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.368 r_dihedral_angle_1_deg 21.628 r_dihedral_angle_3_deg 18.883 r_dihedral_angle_4_deg 17.518 r_lrange_it 6.612 r_lrange_other 6.61 r_mcangle_it 3.925 r_mcangle_other 3.925 r_scangle_it 3.615 r_scangle_other 3.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.368 r_dihedral_angle_1_deg 21.628 r_dihedral_angle_3_deg 18.883 r_dihedral_angle_4_deg 17.518 r_lrange_it 6.612 r_lrange_other 6.61 r_mcangle_it 3.925 r_mcangle_other 3.925 r_scangle_it 3.615 r_scangle_other 3.615 r_mcbond_it 2.372 r_mcbond_other 2.372 r_scbond_it 2.192 r_scbond_other 2.192 r_angle_refined_deg 1.525 r_angle_other_deg 1.169 r_symmetry_nbd_refined 0.327 r_nbd_other 0.248 r_nbd_refined 0.185 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.168 r_ncsr_local_group_3 0.086 r_ncsr_local_group_1 0.081 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_2 0.068 r_chiral_restr 0.055 r_symmetry_xyhbond_nbd_refined 0.043 r_symmetry_xyhbond_nbd_other 0.014 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8047 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing