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X-ray structure of Perm2, a circularly permuted mutant of the sweet protein MNEI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Precipitant: 19% (w/v) PEG 4000, 19% (v/v) 2-Propanol
Buffer: 0.095 M Trisodium citrate (pH 5.5)
Additive: 5% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.23 44.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.464 α = 90 b = 32.518 β = 97.84 c = 40.824 γ = 90
Symmetry Space Group P 1 2 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 PIXEL DECTRIS EIGER X 16M 2022-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.26 39.1 85.59 0.06587 0.07209 0.02871 0.993 14.46 6.3 23712 21.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.264 1.31 37.35 0.8873 0.4936 0.68 1.05 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.26 39.1 1.95 23710 457 85.59 0.1598 0.1591 0.159 0.1916 0.192 35.56
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 f_dihedral_angle_d 5.6363 f_angle_d 0.8932 f_chiral_restr 0.0741 f_plane_restr 0.017 f_bond_d 0.0109
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 802 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing