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Crystal structure at 1.45- resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GHS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 Sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.034 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.27 α = 90 b = 53.93 β = 90 c = 113.55 γ = 90
Symmetry Space Group P 21 21 21
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 4 2002-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.45 20 97.7 0.035 0.035 13.4 3.6 53238 52014 10.46
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) 1.45 1.5 97.7 0.129 0.129 5.6 3.6 4819
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1GHS 1.45 20 52014 49317 2644 97.4 0.15835 0.15835 0.15722 0.1601 0.1794 0.1826 RANDOM 14.92
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 r_dihedral_angle_1_deg 6.01 r_scangle_it 1.938 r_scbond_it 1.206 r_angle_refined_deg 1.095 r_angle_other_deg 0.787 r_mcangle_it 0.761 r_mcbond_it 0.384 r_nbd_other 0.229 r_nbd_refined 0.195 r_symmetry_vdw_other 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.01 r_scangle_it 1.938 r_scbond_it 1.206 r_angle_refined_deg 1.095 r_angle_other_deg 0.787 r_mcangle_it 0.761 r_mcbond_it 0.384 r_nbd_other 0.229 r_nbd_refined 0.195 r_symmetry_vdw_other 0.188 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.118 r_symmetry_vdw_refined 0.097 r_nbtor_other 0.078 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2395 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling AMoRE phasing