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Crystal structure of a pro-inflammatory lectin from the seeds of Dioclea wilsonii STANDL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.01 M Nickel (II), 0.1 M Tris pH 8.0, 1.0 M lithium sulfate monohydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.82 α = 90 b = 66.873 β = 90 c = 107.345 γ = 90
Symmetry Space Group I 2 2 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 MAR CCD 165 mm 2010-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.47 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 20 93.6 0.046 0.046 9392 9238 2 2 29.7
Refinement Statistics Diffraction ID Structure Solution Method 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 MOLECULAR REPLACEMENT 2.3 19.431 1.34 9392 9238 446 94.99 0.2162 0.2138 0.2128 0.2615 0.2545 22.668
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] 6.192 -1.6972 -4.4948
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.826 f_angle_d 1.155 f_chiral_restr 0.066 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1778 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 33
Software Software Software Name Purpose SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection XSCALE data scaling