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Crystal Structure of Hemolytic Lectin CEL-III Complexed with methyl-alpha-D-galactopylanoside
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 METHYL-ALPHA-D-GALACTOPYLANOSIDE, 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 2.32 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.287 α = 90 b = 65.451 β = 97.07 c = 126.993 γ = 90
Symmetry Space Group P 1 21 1
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 1.95 125.99 100 0.077 14.1 3.7 63509 25.3
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) 1.95 2.06 100 0.255 3.8 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VCL 1.95 58.12 60266 3221 100 0.19311 0.19061 0.23926 0.2486 RANDOM 29.578
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 39.906 r_dihedral_angle_4_deg 16.827 r_dihedral_angle_3_deg 14.598 r_dihedral_angle_1_deg 6.509 r_scangle_it 2.997 r_scbond_it 1.919 r_angle_refined_deg 1.317 r_mcangle_it 1.276 r_mcbond_it 0.77 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.906 r_dihedral_angle_4_deg 16.827 r_dihedral_angle_3_deg 14.598 r_dihedral_angle_1_deg 6.509 r_scangle_it 2.997 r_scbond_it 1.919 r_angle_refined_deg 1.317 r_mcangle_it 1.276 r_mcbond_it 0.77 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.184 r_symmetry_vdw_refined 0.17 r_chiral_restr 0.093 r_metal_ion_refined 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6618 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing