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Atomic structure of the beta-trefoil domain of the Laccaria bicolor lectin LBL in complex with lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y9F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% (w/v) PEG 6000, 0.1 M sodium acetate, pH 5.0, and 0.2 M ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.14 42.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.53 α = 90 b = 61.27 β = 90 c = 44.79 γ = 90
Symmetry Space Group P 21 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 MARMOSAIC 225 mm CCD 2011-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 15.2 100 0.123 0.044 0.988 10.9 8 79659 5.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.05 0.123 0.044 0.988
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT FREE R-VALUE 2y9f 1 15.2 1.36 79600 3995 99.98 0.1408 0.1402 0.1403 0.1523 0.1527 9.85
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.1446 f_angle_d 1.2686 f_chiral_restr 0.0857 f_plane_restr 0.0143 f_bond_d 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1184 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 138
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PHASER phasing