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Crystal structure of Calsepa lectin in complex with bisected glycan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Hepes-Na (pH 7.5), 3.0 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.608 α = 90.01 b = 52.836 β = 90.03 c = 54.774 γ = 94.05
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2014-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
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 1.85 100 97 0.088 16.7 1.9 44270
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 1.85 1.88 96 0.452 1.9 2
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 1OUW 1.85 54.77 41846 2234 96.84 0.24712 0.24542 0.2461 0.27877 0.2791 RANDOM 23.096
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] -0.31 -1.66 -0.05 -0.09 -0.1 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.397 r_dihedral_angle_4_deg 17.848 r_dihedral_angle_3_deg 12.645 r_dihedral_angle_1_deg 5.991 r_long_range_B_refined 3.824 r_mcangle_it 1.934 r_mcbond_it 1.096 r_angle_refined_deg 1.079 r_scbond_it 1.015 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.397 r_dihedral_angle_4_deg 17.848 r_dihedral_angle_3_deg 12.645 r_dihedral_angle_1_deg 5.991 r_long_range_B_refined 3.824 r_mcangle_it 1.934 r_mcbond_it 1.096 r_angle_refined_deg 1.079 r_scbond_it 1.015 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 4335 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing