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Crystal structure of L-selectin lectin/EGF domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100 mM sodium cacodylate pH 7.5, 200 mM calcium acetate, 40% (v/v) PEG 600
Crystal Properties Matthews coefficient Solvent content 3.78 67.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.598 α = 90 b = 118.598 β = 90 c = 118.598 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 CCD RAYONIX MX-225 2017-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.94 31.7 99.87 16.82 5.5 20674
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3CFW 1.94 31.697 2.03 20673 1034 99.9 0.2034 0.2018 0.2311 0.2335
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 9.192 f_angle_d 0.9 f_chiral_restr 0.053 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1257 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data scaling PHENIX phasing XDS data reduction