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Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291.15 0.1 M NaAc
0.1 M MES pH 6.5
30% (w/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.096 α = 90 b = 104.271 β = 90 c = 148.739 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 MARMOSAIC 300 mm CCD Vertical Focusing Mirror 2015-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 30 99.3 0.173 0.185 0.089 5.7 7.5 89308
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.01 98.6 0.508 0.782 7.6 7305
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 5KXC 1.95 30 84025 4358 98.2 0.1798 0.1789 0.1878 0.1981 0.2056 RANDOM 22.833
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] 0.25 0.44 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_dihedral_angle_4_deg 22.669 r_dihedral_angle_3_deg 12.767 r_dihedral_angle_1_deg 6.927 r_mcangle_it 2.311 r_angle_refined_deg 1.566 r_mcbond_it 1.48 r_mcbond_other 1.466 r_angle_other_deg 0.998 r_chiral_restr 0.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_dihedral_angle_4_deg 22.669 r_dihedral_angle_3_deg 12.767 r_dihedral_angle_1_deg 6.927 r_mcangle_it 2.311 r_angle_refined_deg 1.566 r_mcbond_it 1.48 r_mcbond_other 1.466 r_angle_other_deg 0.998 r_chiral_restr 0.179 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7404 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 326
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction