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Structure of the human LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain in an unliganded state
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.5M NaCl, 0.1M Sodium/Potassium Phosphate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.95 58.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.81 α = 90 b = 70.81 β = 90 c = 75.77 γ = 90
Symmetry Space Group P 41 21 2
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 2017-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.64 41.77 100 0.059 1 21 12.5 303577 30.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.67 1.951 0.5 1.2
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 SAD FREE R-VALUE 1.64 41.77 1.34 24215 1180 99.97 0.1845 0.1826 0.185 0.2228 0.2227 39.97
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 16.352 f_angle_d 0.9686 f_chiral_restr 0.0621 f_plane_restr 0.0064 f_bond_d 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 944 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 40
Software Software Software Name Purpose xia2 data scaling PHENIX phasing PHENIX refinement Coot model building