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Canavalia villosa lectin in complex with alpha-methyl-mannoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L8Q Canavalia grandiflora lectin (ConGr) lectin complexed with X-MAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.2 298 PEG1000, potassium citrate phosphate, lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.25 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.49 α = 90 b = 84.44 β = 90 c = 89.07 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 PIXEL DECTRIS PILATUS 2M 2017-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 27.48 99.8 0.112 0.126 0.056 0.991 8.9 4.9 8301
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.7 0.433 0.489 0.224 0.867 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 27.48 1.34 8295 408 99.63 0.1848 0.1813 0.2489 0.25
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 13.951 f_angle_d 0.998 f_chiral_restr 0.057 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1784 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing