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High resolution structure of VEGF-A 12:107 crystallized in tetragonal form
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 8.5 293 (VEGF)2:2 PEPTIDE_2C COMPLEX PURIFIED ON SEC AND CONCENTRATED AT 17MG/ML IN TRIS/HCL 10MM PH 8.5. (SEE ID 6Z3F) mix 1UL OF COMPLEX WITH 1 UL OF RESERVOIR : TRIS/HCL 100MM PH 8.5 / MPD 42% (V/V) / (NH4)2PO4 200MM
Crystal Properties Matthews coefficient Solvent content 3.51 64.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.34 α = 90 b = 88.34 β = 90 c = 40.489 γ = 90
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 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 44.17 99.6 0.044 0.092 0.049 0.996 7.9 3.3 41413 18.43
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 99.7 0.693 0.838 0.464 0.707 1.6 3.1
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 44.17 1.34 41352 2069 99.45 0.1652 0.1641 0.1658 0.186 0.1875 29.99
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 18.1176 f_angle_d 1.0231 f_chiral_restr 0.0605 f_bond_d 0.0095 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1558 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection SCALA data scaling PHENIX phasing XDS data reduction