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Room temperature structure of concanavalin A complexed to bivalent ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 pH 6
Crystal Properties Matthews coefficient Solvent content 3.66 66.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.1 α = 90 b = 127.4 β = 90 c = 118.9 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE NONIUS MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 2.66 26 96.8 0.072 0.072 2.5 21164 28.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CNA 2.66 26 21164 2143 96.8 0.176 0.1753 0.2 0.2012 RANDOM 28.9
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] -5.66 1.35 4.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 3.02 c_mcangle_it 2.65 c_scbond_it 1.97 c_angle_deg 1.7 c_mcbond_it 1.5 c_improper_angle_d 0.84 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 3.02 c_mcangle_it 2.65 c_scbond_it 1.97 c_angle_deg 1.7 c_mcbond_it 1.5 c_improper_angle_d 0.84 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3618 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 57
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement