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X-ray structure of the CCL2 lectin in complex with sialyl lewis X
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LIE PDB ENTRY 2LIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 MIDAS 2-28. 30% GLYCEROL ETHOXYLATE AND 0.1M TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.34 47.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.68 α = 90 b = 121.68 β = 90 c = 144.907 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS PILATUS 2013-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.95 29.23 99.2 0.05 18 6.3 46087 2
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 1.95 2 100 0.42 4.4 6.6
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 2LIE 1.95 29.85 43754 2327 98.8 0.1765 0.17504 0.1839 0.20433 0.2135 RANDOM 48.158
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] -0.84 -0.42 -0.84 2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.018 r_dihedral_angle_4_deg 14.476 r_dihedral_angle_3_deg 10.934 r_dihedral_angle_1_deg 6.386 r_mcangle_it 2.058 r_scbond_it 1.746 r_angle_refined_deg 1.608 r_mcbond_it 1.376 r_mcbond_other 1.376 r_angle_other_deg 1.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.018 r_dihedral_angle_4_deg 14.476 r_dihedral_angle_3_deg 10.934 r_dihedral_angle_1_deg 6.386 r_mcangle_it 2.058 r_scbond_it 1.746 r_angle_refined_deg 1.608 r_mcbond_it 1.376 r_mcbond_other 1.376 r_angle_other_deg 1.312 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 3991 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing