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Structure of the Mus musclus Langerin carbohydrate recognition domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 0.1 M MES, pH 6.0, 30% (v/v) polyethylene glycol 600, 5% (w/v) polyethylene glycol 1000, and 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.5 64.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.31 α = 90 b = 143.31 β = 90 c = 143.31 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 SAGITALLY FOCUSED SI(111) 2016-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 50 100 0.78 0.958 4.8 20 19343
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.54 99.9 2.1 19.5
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 3KQG 2.4 45.32 18368 972 99.97 0.19792 0.19604 0.23384 0.1652 RANDOM 52.106
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] -73.59 -42.91 -40.26 68.12 -27.14 5.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.101 r_dihedral_angle_3_deg 15.991 r_dihedral_angle_4_deg 14.336 r_dihedral_angle_1_deg 6.649 r_long_range_B_refined 5.355 r_mcangle_it 2.568 r_scbond_it 1.661 r_mcbond_it 1.626 r_angle_refined_deg 1.237 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.101 r_dihedral_angle_3_deg 15.991 r_dihedral_angle_4_deg 14.336 r_dihedral_angle_1_deg 6.649 r_long_range_B_refined 5.355 r_mcangle_it 2.568 r_scbond_it 1.661 r_mcbond_it 1.626 r_angle_refined_deg 1.237 r_chiral_restr 0.093 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other 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 80 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing