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The crystal structure of Sclerotium Rolfsii lectin variant 2 (SSR2) in complex with N-acetyl-glucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 20% v/v MPD
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.025 α = 90 b = 100.025 β = 90 c = 63.783 γ = 90
Symmetry Space Group P 42 21 2
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 AGILENT ATLAS CCD 2013-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 13.95 99.9 0.097 13.1 6.7 36058
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 99.9 2.3 4.1
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 2OFE 1.7 13.95 34261 1796 99.74 0.16682 0.16495 0.1765 0.20329 0.2092 RANDOM 11.981
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] 0.31 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.41 r_dihedral_angle_3_deg 11.542 r_dihedral_angle_4_deg 10.699 r_dihedral_angle_1_deg 6.57 r_long_range_B_refined 5.293 r_long_range_B_other 5.293 r_scangle_other 1.964 r_angle_other_deg 1.549 r_angle_refined_deg 1.486 r_mcangle_it 1.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.41 r_dihedral_angle_3_deg 11.542 r_dihedral_angle_4_deg 10.699 r_dihedral_angle_1_deg 6.57 r_long_range_B_refined 5.293 r_long_range_B_other 5.293 r_scangle_other 1.964 r_angle_other_deg 1.549 r_angle_refined_deg 1.486 r_mcangle_it 1.407 r_mcangle_other 1.406 r_scbond_it 1.206 r_scbond_other 1.205 r_mcbond_it 0.836 r_mcbond_other 0.826 r_chiral_restr 0.179 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2282 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling PHENIX phasing