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Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo trimannoside mimic.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IT6 PDB ENTRY 2IT6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 VAPOR DIFFUSION, HANGING DROP, 293K. 35% PEG 3350, 200MM NACL, 100MM CACODYLATE PH 6.5, CRYOPROTECTED IN PARATONE-N
Crystal Properties Matthews coefficient Solvent content 1.8 31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.33 α = 90 b = 71.33 β = 90 c = 52.666 γ = 90
Symmetry Space Group P 43 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 CCD ADSC CCD MIRRORS 2010-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.35 50.44 99.9 0.06 20.13 7.34 30348 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.43 99.9 0.42 4.82 7.3
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 PDB ENTRY 2IT6 1.35 50.44 28812 1536 99.87 0.14808 0.14704 0.16786 0.1712 RANDOM 14.112
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] 0.09 0.09 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.033 r_dihedral_angle_4_deg 25.292 r_dihedral_angle_3_deg 13.901 r_dihedral_angle_1_deg 7.196 r_rigid_bond_restr 7.085 r_scangle_it 4.879 r_scbond_it 3.569 r_mcangle_it 2.644 r_angle_refined_deg 1.791 r_mcbond_it 1.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.033 r_dihedral_angle_4_deg 25.292 r_dihedral_angle_3_deg 13.901 r_dihedral_angle_1_deg 7.196 r_rigid_bond_restr 7.085 r_scangle_it 4.879 r_scbond_it 3.569 r_mcangle_it 2.644 r_angle_refined_deg 1.791 r_mcbond_it 1.555 r_nbtor_refined 0.321 r_nbd_refined 0.255 r_symmetry_vdw_refined 0.228 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.176 r_metal_ion_refined 0.117 r_chiral_restr 0.116 r_gen_planes_refined 0.017 r_bond_refined_d 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1051 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing