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Structure of the lectin from Platypodium elegans in complex with heptasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 10% PEG20K, 2% DIOXANE, 100 MM BICINE PH 9, 30% GLYCEROL ADDED AS CRYOPROTECTANT.
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.4 α = 90 b = 76.98 β = 90 c = 125.59 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 SX-165 2010-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.65 47.56 91.4 0.05 13.6 3.4 55022 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 1.65 1.74 65.8 0.25 3.9 2.6
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 IN30 1.65 47.57 52116 2760 90.28 0.15724 0.1556 0.1638 0.18816 0.1969 RANDOM 11.044
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] -0.03 0.69 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.693 r_dihedral_angle_4_deg 20.989 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_1_deg 7.292 r_scangle_it 3.695 r_scbond_it 2.328 r_mcangle_it 1.635 r_angle_refined_deg 1.595 r_mcbond_it 0.918 r_angle_other_deg 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.693 r_dihedral_angle_4_deg 20.989 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_1_deg 7.292 r_scangle_it 3.695 r_scbond_it 2.328 r_mcangle_it 1.635 r_angle_refined_deg 1.595 r_mcbond_it 0.918 r_angle_other_deg 0.91 r_mcbond_other 0.26 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 3802 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 223
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing