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Crystal structure of the Rhizoctonia solani agglutinin in complex with N'-acetyl-galactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G9M PDB ENTRY 4G9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 289 Reservoir: 0.1 M sodium acetate, pH 4.2, 20% v/v PEG8000, 0.2 M sodium chloride, 10 mM sodium citrate, a single native crystal was soaked in a solution of 12.9 mM N'-acetyl-galactosamine (GalNAc) in reservoir solution for 48 hours, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 41.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.583 α = 90 b = 61.251 β = 93.45 c = 32.839 γ = 90
Symmetry Space Group C 1 2 1
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 2012-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54178
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 2.2 13.86 99.5 0.101 11.5 4.33 13153 13153 10.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.37 99.3 0.254 5.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS PDB ENTRY 4G9M 2.2 13.859 1.35 13153 13153 646 99.88 0.1543 0.1502 0.1511 0.2316 0.2316
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] -2.1351 -1.1153 1.3682 0.767
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.343 f_angle_d 1.137 f_chiral_restr 0.077 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2177 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement REFMAC refinement CrysalisPro data collection CrysalisPro data reduction SCALA data scaling REFMAC phasing