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Structure of the human LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain bound with decasaccharide hyaluronan.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously solved apo structure of the same protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20 %w/v Polyethylene Glycol 3350, 0.1 M bis-Tris Propane pH 6.5, 0.2 M Sodium Malonate
Crystal Properties Matthews coefficient Solvent content 1.76 30.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.59 α = 90 b = 53.26 β = 90 c = 53.74 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 100 PIXEL DECTRIS EIGER X 9M 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.32 53.3 99.4 0.084 1 15.4 10.4 27202 16.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.69 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.32 37.83 1.34 27199 1385 99.36 0.1748 0.1724 0.173 0.2173 0.2177 25.92
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 13.5603 f_angle_d 1.2935 f_chiral_restr 0.0911 f_bond_d 0.0122 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 910 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 120
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing
EM Software Task Software Package Version MODEL REFINEMENT PHENIX 1.21rc1_4899