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Crystal Structure of Hemolytic Lectin CEL-III Complexed with GalNac
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 10mM GalNac, 12% PEG 8000, 100mM Bis-Tris/NaOH, 200mM magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.637 α = 85.3 b = 65.169 β = 73.55 c = 66.675 γ = 89.94
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE BRUKER DIP-6040B 2004-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.7 64.96 96.4 0.067 10.6 2 89844 19.4
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) 1.7 1.79 95.2 0.166 3.5 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 1VCL 1.7 64.96 85355 4489 96.43 0.18618 0.18455 0.1841 0.21752 0.2171 RANDOM 20.532
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.897 r_dihedral_angle_4_deg 15.132 r_dihedral_angle_3_deg 14.078 r_dihedral_angle_1_deg 7.652 r_scangle_it 3.304 r_scbond_it 2.178 r_angle_refined_deg 1.46 r_mcangle_it 1.34 r_mcbond_it 0.866 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.897 r_dihedral_angle_4_deg 15.132 r_dihedral_angle_3_deg 14.078 r_dihedral_angle_1_deg 7.652 r_scangle_it 3.304 r_scbond_it 2.178 r_angle_refined_deg 1.46 r_mcangle_it 1.34 r_mcbond_it 0.866 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.274 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.105 r_metal_ion_refined 0.058 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6610 Nucleic Acid Atoms Solvent Atoms 838 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing