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Structure of DC-SIGNR and a portion of repeat domain 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K9J PDB ENTRY 1K9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 100mM MgCl2, 100mM Na Cacodylate, 12% PEG 3000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.8 32.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.233 α = 90 b = 54.887 β = 90 c = 62.352 γ = 90
Symmetry Space Group P 21 21 21
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 CUSTOM-MADE 2001-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0395 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.41 31.4 97.5 0.069 25340 25340
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.41 1.48 99.2 0.222 5.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1K9J 1.41 31.4 23999 1290 97.6 0.17698 0.17613 0.1847 0.19295 0.1994 RANDOM 11.071
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] 0.18 -0.28 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.49 r_scangle_it 3.975 r_scbond_it 2.491 r_mcangle_it 1.795 r_angle_refined_deg 1.366 r_mcbond_it 0.964 r_angle_other_deg 0.828 r_symmetry_vdw_other 0.367 r_nbd_refined 0.319 r_nbd_other 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.49 r_scangle_it 3.975 r_scbond_it 2.491 r_mcangle_it 1.795 r_angle_refined_deg 1.366 r_mcbond_it 0.964 r_angle_other_deg 0.828 r_symmetry_vdw_other 0.367 r_nbd_refined 0.319 r_nbd_other 0.25 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.084 r_nbtor_other 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1141 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing