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Structure of the Mus musclus Langerin carbohydrate recognition domain in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M MES, pH 6.0, 30% (v/v) polyethylene glycol 600, 5% (w/v) polyethylene glycol 1000, and 10% (v/v) glycerol, 5% Glucose
Crystal Properties Matthews coefficient Solvent content 3.58 65.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.42 α = 90 b = 144.42 β = 90 c = 144.42 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 6M 2016-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.7 50 100 0.114 0.116 1 28.2 40.4 54929 29.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 100 1.761 1.783 0.85 3.2 41.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5K8Y 1.7 45.67 52330 2593 100 0.14485 0.14385 0.16436 0.2075 RANDOM 28.054
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] -19.73 2.23 -2.01 10.17 -39.82 9.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.755 r_dihedral_angle_4_deg 16.591 r_dihedral_angle_3_deg 12.216 r_dihedral_angle_1_deg 6.686 r_long_range_B_refined 3.844 r_long_range_B_other 3.844 r_angle_refined_deg 1.398 r_scangle_other 1.345 r_mcangle_it 1.065 r_mcangle_other 1.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.755 r_dihedral_angle_4_deg 16.591 r_dihedral_angle_3_deg 12.216 r_dihedral_angle_1_deg 6.686 r_long_range_B_refined 3.844 r_long_range_B_other 3.844 r_angle_refined_deg 1.398 r_scangle_other 1.345 r_mcangle_it 1.065 r_mcangle_other 1.064 r_angle_other_deg 0.98 r_scbond_it 0.856 r_scbond_other 0.855 r_mcbond_it 0.665 r_mcbond_other 0.665 r_chiral_restr 0.195 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2224 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing