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L-SIGN CRD in complex with Man84.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystallization technique: sitting drop of 150 nL (ratio 2:1, protein:precipitant).
Protein stock: 20 mg / mL into 150 mM NaCl, 25 mM TRIS 8, 4 mM CaCl2.
200 nL
Precipitant: PEG Suite Qiagen H12 (0.18 M tri-Ammonium citrate, 20 %(w/v) PEG 3350).
Crystal Properties Matthews coefficient Solvent content 1.79 31.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.43 α = 90 b = 48.89 β = 103.53 c = 35.67 γ = 90
Symmetry Space Group P 1 21 1
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 2023-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 48.88 97.5 0.996 9.25 3.15 10206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 0.624
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 34.68 9695 511 97.62 0.16529 0.16257 0.1727 0.2175 0.2279 RANDOM 26.935
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] -0.32 1.67 -1.52 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.475 r_dihedral_angle_4_deg 18.65 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 7.231 r_long_range_B_refined 5.723 r_long_range_B_other 5.64 r_scangle_other 3.389 r_mcangle_other 2.919 r_mcangle_it 2.917 r_scbond_it 2.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.475 r_dihedral_angle_4_deg 18.65 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 7.231 r_long_range_B_refined 5.723 r_long_range_B_other 5.64 r_scangle_other 3.389 r_mcangle_other 2.919 r_mcangle_it 2.917 r_scbond_it 2.248 r_scbond_other 2.247 r_mcbond_it 1.901 r_mcbond_other 1.897 r_angle_refined_deg 1.508 r_angle_other_deg 1.43 r_chiral_restr 0.501 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 1100 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 26
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing Coot model building REFMAC refinement