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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 3R50 PDB entry 3R50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 0.05 M sodium acetate, 0.05 M cadmium chloride, 15% polyethylene glycol 400 (PEG 400) against a reservoir of 0.1 M sodium acetate, 0.1 M cadmium chloride, 30% PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.15 42.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.28 α = 90 b = 83.71 β = 112.76 c = 65.06 γ = 90
Symmetry Space Group P 1 21 1
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 210 mirrors 2009-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
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 2.1 30 97 0.064 16.28 3.1 33243 8.5
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 2.1 2.18 93.5 0.269 3.6 2.7 3172
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 3R50 2.1 25.98 32172 3216 93.8 0.188 0.188 0.1842 0.243 0.242 RANDOM 27.5
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] -1.61 4.84 0.82 0.79
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.2 c_scangle_it 3.14 c_mcangle_it 2.7 c_scbond_it 2.14 c_mcbond_it 1.66 c_angle_deg 1.5 c_improper_angle_d 0.88 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.2 c_scangle_it 3.14 c_mcangle_it 2.7 c_scbond_it 2.14 c_mcbond_it 1.66 c_angle_deg 1.5 c_improper_angle_d 0.88 c_bond_d 0.01 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 4625 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 55
Software Software Software Name Purpose ADSC data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing