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The 15k neutron structure of saccharide-free concanavalin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 1.65 A X-ray model of D20-grown saccharide-free concacanavalin A at 100K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH DIALYSIS 6.5 293 0.1M NaNO3, 0.05M Tris-acetate, 1mM MnCl2, 1mM CaCl2 (all in D2O), pH 6.50, BATCH DIALYSIS, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.4 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.16 α = 90 b = 86.129 β = 90 c = 61.594 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 neutron 15 IMAGE PLATE 2000-11-16 L QUASI LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 2.8-3.8
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 2.5 32.82 74.4 0.235 0.235 5.6 4.7 6462 6339 2 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.64 54.2 0.358 0.358 2.3 2.6 651
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free Selection Details Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65A X-ray model of D20-grown saccharide-free concacanavalin A at 100K 2.5 32.82 2 6462 6339 331 74.4 0.266 0.266 0.32 RANDOM 24.9
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] -7.8 12.54 -4.74
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.7 c_improper_angle_d 7.31 c_mcangle_it 2.09 c_scangle_it 1.68 c_angle_deg 1.6 c_mcbond_it 1.2 c_scbond_it 1.09 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.7 c_improper_angle_d 7.31 c_mcangle_it 2.09 c_scangle_it 1.68 c_angle_deg 1.6 c_mcbond_it 1.2 c_scbond_it 1.09 c_bond_d 0.006 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 3564 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 2
Software Software Software Name Purpose LAUEGEN/LSCALE data collection SCALA data reduction CNS refinement LAUEGEN/LSCALE data reduction CCP4 data scaling CNS phasing