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VEGF-A 13:107 crystallized with 4C 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 4.5 293 (VEGF)2:2 PEPTIDE_4C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. MIX 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : NAOAC/HCL 100MM PH 4.5 /
MPD 35% (V/V) / (NH4)2PO4 150MM
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.075 α = 90 b = 55.603 β = 90 c = 77.073 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 PILATUS3 2M 2016-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.272 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 55.6 100 0.077 0.082 0.027 0.999 11.3 8.8 31383 21.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 100 0.682 0.726 0.246 0.966 2.4
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 1.6 45.09 1.33 31207 1594 99.56 0.2054 0.2036 0.2094 0.2415 0.2477 42.79
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 20.4847 f_angle_d 1.2647 f_chiral_restr 0.0618 f_bond_d 0.01 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1669 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction SCALA data scaling PHENIX phasing