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crystal structure of recombinant DiocleA grandiflora lectin mutant E123A-H131N-K132Q complexed witH 5-bromo-4-chloro-3-indolyl-a-D- mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JE9 PDB ENTRY 2JE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 18% PEG 8000, 0.1M CACODYLATE, PH 6.5 AND 0.2M ZINC ACETATE
Crystal Properties Matthews coefficient Solvent content 2.61 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.194 α = 90 b = 84.552 β = 90 c = 176.21 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 MARRESEARCH 2006-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 2 28.9 99.6 0.07 12.9 3.8 73352 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 2 2.11 100 0.25 3 3.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2JE9 2 88.04 69591 3702 99.5 0.182 0.179 0.1806 0.23 RANDOM 19.04
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] 0.06 0.61 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.168 r_dihedral_angle_4_deg 13.407 r_dihedral_angle_3_deg 12.68 r_dihedral_angle_1_deg 7.742 r_angle_refined_deg 1.508 r_nbtor_refined 0.301 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.168 r_dihedral_angle_4_deg 13.407 r_dihedral_angle_3_deg 12.68 r_dihedral_angle_1_deg 7.742 r_angle_refined_deg 1.508 r_nbtor_refined 0.301 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.104 r_metal_ion_refined 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 7223 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing