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Crystal structure of a bispecific DutaFab in complex with human PDGF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 DutaFab and PDGF-BB (Peprotech, catalogue number 100-13A) were mixed at a 1:1 molar ratio in relation to PDGF monomer. The complex was concentrated to 12 mg/ml and crystallization was performed by hanging drop vapour diffusion against 0.1 M Tris pH 7.5, 42 % 2-methyl-2,4-pentanediol (MPD) at 20 C. Plate-shaped crystals grew within a few weeks and were frozen in liquid nitrogen with 20% glycerol as cryo-protectant.
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.301 α = 90 b = 75.474 β = 110.584 c = 116.505 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 PIXEL DECTRIS PILATUS3 6M 2015-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9760 Diamond I03
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 2.989 30 97.7 0.162 7.3 3 29016 43.9
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 2.989 3.2 92.8 0.773 1.8 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 4QCI 2.989 29.735 29016 1451 97.832 0.256 0.2531 0.3044 0.26 62.916
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] 6.669 -6.372 -3.405 1.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.015 r_dihedral_angle_3_deg 19.121 r_dihedral_angle_4_deg 16.836 r_lrange_it 14.031 r_mcangle_it 8.908 r_scangle_it 8.836 r_dihedral_angle_1_deg 8.151 r_mcbond_it 5.489 r_scbond_it 5.338 r_angle_refined_deg 1.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.015 r_dihedral_angle_3_deg 19.121 r_dihedral_angle_4_deg 16.836 r_lrange_it 14.031 r_mcangle_it 8.908 r_scangle_it 8.836 r_dihedral_angle_1_deg 8.151 r_mcbond_it 5.489 r_scbond_it 5.338 r_angle_refined_deg 1.448 r_nbtor_refined 0.312 r_nbd_refined 0.261 r_symmetry_xyhbond_nbd_refined 0.2 r_symmetry_nbd_refined 0.189 r_xyhbond_nbd_refined 0.183 r_ncsr_local_group_3 0.112 r_chiral_restr 0.108 r_ncsr_local_group_2 0.069 r_ncsr_local_group_1 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7935 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing