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X-ray structure of Perm3, 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 5.6 291 Precipitant: 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol
Buffer: 0.085 M Sodium citrate (pH 5.6)
Salt: 0.17 M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.451 α = 90 b = 32.446 β = 97.58 c = 41.484 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 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 1.15 30.41 92.61 0.0624 0.0683 0.0273 0.996 15.22 6.1 34452 13.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.24 75.33 0.5609 0.6323 0.2841 0.9 2.17
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 1.15 30.41 1.95 34452 644 92.61 0.1595 0.159 0.1589 0.1874 0.1872 21.26
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 12.7445 f_angle_d 0.7276 f_chiral_restr 0.0721 f_plane_restr 0.0104 f_bond_d 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 793 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing