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Resolution of the structure of the allergenic and antifungal banana fruit thaumatin-like protein at 1.7A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1THV PDB entry 1THV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 PEG 4000, Ammonium Sulfate, Sodium Acatate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.3 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.844 α = 90 b = 52.839 β = 90 c = 80.606 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 IMAGE PLATE MARRESEARCH 2002-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 42.2 96.9 0.042 17.6 4.6 20728 20095 15.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 94.9 0.131 9.4 4.3 1920
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 PDB entry 1THV 1.7 20 20728 20067 1027 96.9 0.14426 0.14426 0.14248 0.1498 0.17712 0.1434 RANDOM 12.877
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] -0.63 0.15 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.325 r_scangle_it 3.084 r_scbond_it 1.925 r_angle_refined_deg 1.354 r_mcangle_it 1.125 r_angle_other_deg 0.808 r_mcbond_it 0.61 r_symmetry_vdw_other 0.331 r_nbd_other 0.251 r_nbd_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.325 r_scangle_it 3.084 r_scbond_it 1.925 r_angle_refined_deg 1.354 r_mcangle_it 1.125 r_angle_other_deg 0.808 r_mcbond_it 0.61 r_symmetry_vdw_other 0.331 r_nbd_other 0.251 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.202 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.083 r_nbtor_other 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1484 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing