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Crystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM HEPES pH 8.0
50 mM Cadmiun Sulfate
1M Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.46 α = 90 b = 85.18 β = 90 c = 174.58 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 PIXEL DECTRIS PILATUS 2M 2015-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.47 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.75 33.84 92.2 0.064 0.064 0.069 0.026 0.998 15.8 6.3 100509 100509 22.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 70.8 0.248 0.047 0.051 0.019 0.969 6 11157
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 4NOT 1.765 33.845 1.33 99788 4959 93.45 0.2185 0.2169 0.218 0.2489 0.2495 26.2792
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 15.938 f_angle_d 1.372 f_chiral_restr 0.067 f_bond_d 0.011 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7024 Nucleic Acid Atoms Solvent Atoms 719 Heterogen Atoms 100
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing