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Crystal structure of VEGF binding IgG1-Fc (Fcab CT6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Morpheus_C6
0.03M of each NPS: (sodium nitrate, disodium hydrogen phosphate, ammonium sulfate).
0.1M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000, 20% v/v ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.49 α = 90 b = 72 β = 90 c = 168.3 γ = 90
Symmetry Space Group P 2 21 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 PIXEL DECTRIS PILATUS3 2M CRL 2015-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.5 48.028 99 0.1254 0.998 7.69 4.4 25171 64.62
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 2.5 2.589 100 1.871 0.74 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5K64 2.5 48.028 1.2 46529 3709 97.96 0.223 0.221 0.2269 0.2463 0.2503
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.446 f_angle_d 0.633 f_chiral_restr 0.045 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3469 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 146
Software Software Software Name Purpose EDNA data collection XDS data reduction XDS data scaling PHENIX phasing PHENIX refinement