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Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X1X PDB ENTRIES 2X1X, 1FLT AND 2E9W experimental model PDB 1FLT PDB ENTRIES 2X1X, 1FLT AND 2E9W experimental model PDB 2E9W PDB ENTRIES 2X1X, 1FLT AND 2E9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 SITTING DROPS AT ROOM TEMPERATURE OVER A RESERVOIR SOLUTION OF 0.1 M BIS-TRIS BUFFER AT PH 8.5-9.5 AND 1.0-1.5 M AMMONIUM SULPHATE.
Crystal Properties Matthews coefficient Solvent content 5.2 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.66 α = 90 b = 166.66 β = 90 c = 166.66 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 PILATUS 6M 2011-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 4.2 30 99.6 0.05 20.9 9.9 5765 -3
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 4.2 4.4 100 1.49 2.1 10.5
Refinement Statistics Diffraction ID Structure Solution 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 MIRAS PDB ENTRIES 2X1X, 1FLT AND 2E9W 4.201 19.92 2 5721 572 100 0.338 0.3341 0.3344 0.3718 0.3659 135.9
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 15.257 f_angle_d 1.032 f_chiral_restr 0.061 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 84
Software Software Software Name Purpose XDS data reduction XDS data scaling autoSHARP phasing MOLREP phasing PHENIX refinement