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VEGF-A 13:107 crystallized with 3C bicyclic peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FLT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 (VEGF)2:2 peptide_3C complex purified on SEC and concentrated at 9.8mg/ml in Tris/HCl 10mM pH 8.5. Mix of 1ul of complex with 1 ul of reservoir : NaOAc/HCl 100mM pH 4.6 / MPD 36% (v/v) / CaCl2 20mM
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.256 α = 90 b = 55.691 β = 90 c = 76.979 γ = 90
Symmetry Space Group P 21 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 80 PIXEL DECTRIS PILATUS 2M 2014-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.97625 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.79 45.12 99.8 0.068 0.075 0.03 14.6 6 22364 25.13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.89 97.2 0.704 0.773 0.316 2.4 5.8
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 1FLT 1.8 38.86 1.98 22223 1137 99.93 0.1965 0.1939 0.1964 0.2474 0.2501 36.65
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 21.4314 f_angle_d 1.6223 f_chiral_restr 0.082 f_bond_d 0.0179 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1677 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 37
Software Software Software Name Purpose MxCuBE data collection XDS data reduction SCALA data scaling PHENIX phasing PHENIX refinement