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Structure analysis of a wound-inducible lectin ipomoelin from sweet potato
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OUW PDB ENTRY 1OUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.005 M ferric chloride, 0.05 M sodium citrate, 5% jeffamine M-600 against a reservoir of 0.01 M ferric chloride, 0.1 M sodium citrate, 10% jeffamine M-600, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.34 63.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.486 α = 90 b = 139.468 β = 90 c = 189.873 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 ADSC QUANTUM 315 mirrors 2009-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.27 30 96.6 0.082 18.8 7.3 51599 28.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.35 99.9 0.457 4.65 7.1 5264
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-Factor (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 PDB ENTRY 1OUW 2.27 26.21 49217 2472 91.7 0.202 0.202 0.2022 0.234 0.2354 RANDOM 36.1
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] -6.05 -4.16 10.21
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.2 c_scangle_it 3.07 c_mcangle_it 2.75 c_scbond_it 2.14 c_angle_deg 1.7 c_mcbond_it 1.63 c_improper_angle_d 1.1 c_bond_d 0.015 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.2 c_scangle_it 3.07 c_mcangle_it 2.75 c_scbond_it 2.14 c_angle_deg 1.7 c_mcbond_it 1.63 c_improper_angle_d 1.1 c_bond_d 0.015 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 5794 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing