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Crystal structure OF lecA lectin complexed with a divalent galactoside at 1.65 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKO PDB ENTRY 1OKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 SOLUTION 20 OF THE CSSI SCREEN 8% PEG 20K, 8% PEG550MME, 100 MM TRIS 8.5 AND 0.2 M LI2SO4
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.876 α = 90 b = 66.259 β = 90 c = 159.427 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 MARRESERACH 2013-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 48.47 100 0.04 22.9 5.4 65807 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 1.68 100 0.51 3 5.5
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 1OKO 1.65 48.47 62390 3334 99.91 0.15665 0.15525 0.1678 0.18362 0.193 RANDOM 26.643
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] -0.75 2.17 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.637 r_dihedral_angle_3_deg 10.707 r_dihedral_angle_1_deg 6.041 r_dihedral_angle_4_deg 5.514 r_scbond_it 2.17 r_mcangle_it 1.809 r_angle_refined_deg 1.725 r_mcbond_it 1.201 r_mcbond_other 1.2 r_angle_other_deg 0.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.637 r_dihedral_angle_3_deg 10.707 r_dihedral_angle_1_deg 6.041 r_dihedral_angle_4_deg 5.514 r_scbond_it 2.17 r_mcangle_it 1.809 r_angle_refined_deg 1.725 r_mcbond_it 1.201 r_mcbond_other 1.2 r_angle_other_deg 0.783 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.241 r_nbd_other 0.181 r_nbtor_refined 0.178 r_symmetry_vdw_other 0.178 r_metal_ion_refined 0.154 r_symmetry_hbond_refined 0.133 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.105 r_nbtor_other 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other 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 3614 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing