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X-ray structure of the RSL lectin in complex with Lewis X tetrasaccahride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BT9 PDB ENTRY 2BT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 27% PEG 6K, 0.1 M TRIS, PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.185 α = 90 b = 58.63 β = 90 c = 106.713 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 ADSC CCD 2012-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.8 40.03 99.4 0.08 16.1 5.3 25606 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 1.8 1.84 99.9 0.37 4.1 5.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BT9 1.8 40.03 24275 1304 99.01 0.14743 0.14566 0.1582 0.18021 0.1885 RANDOM 11.752
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] -0.52 -0.5 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.294 r_dihedral_angle_3_deg 10.564 r_dihedral_angle_1_deg 7.019 r_dihedral_angle_4_deg 7.003 r_angle_refined_deg 1.87 r_angle_other_deg 1.851 r_mcangle_it 1.705 r_scbond_it 1.571 r_mcbond_it 1.021 r_mcbond_other 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.294 r_dihedral_angle_3_deg 10.564 r_dihedral_angle_1_deg 7.019 r_dihedral_angle_4_deg 7.003 r_angle_refined_deg 1.87 r_angle_other_deg 1.851 r_mcangle_it 1.705 r_scbond_it 1.571 r_mcbond_it 1.021 r_mcbond_other 1.015 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.01 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 2035 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing