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L-SIGN CRD in complex with Man96.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystallization technique: sitting drop of 100 nL of protein and 50 nL of precipitant).
Protein stock: 20.1 mg/mL, 3.75 mM ligand into 150 mM NaCl, 25 mM TRIS 8, 4 mM CaCl2.
Precipitant: 1-13 of JCSG-plus screen Molecular Dimensions (0.8 M ammonium sulfate, 0.1 M citrate pH 4).
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.72 α = 90 b = 105.72 β = 90 c = 59.11 γ = 120
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 2023-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 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 2 49.66 96.9 0.99 4.66 2.8 24815
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 2 2.05 99 0.733
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 2 49.66 23574 1241 96.93 0.23059 0.22751 0.2638 0.28994 0.32 RANDOM 38.515
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] -2.96 -1.48 -2.96 9.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.508 r_dihedral_angle_2_deg 9.477 r_long_range_B_refined 8.914 r_long_range_B_other 8.88 r_dihedral_angle_1_deg 7.847 r_scangle_other 6.693 r_mcangle_other 5.405 r_mcangle_it 5.391 r_scbond_it 4.456 r_scbond_other 4.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.508 r_dihedral_angle_2_deg 9.477 r_long_range_B_refined 8.914 r_long_range_B_other 8.88 r_dihedral_angle_1_deg 7.847 r_scangle_other 6.693 r_mcangle_other 5.405 r_mcangle_it 5.391 r_scbond_it 4.456 r_scbond_other 4.455 r_mcbond_it 3.659 r_mcbond_other 3.659 r_angle_refined_deg 1.448 r_angle_other_deg 0.531 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2086 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 68
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing Coot model building REFMAC refinement