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X-ray structure of Perm1, 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, SITTING DROP 8.5 291 Precipitant: 25% (w/v) PEG1000, 25% (w/v) PEG3350 and 25% (v/v) (RS)-2-methyl-2,4-pentanediol (MPD)
Buffer: 0.1 M Tris (base); BICINE (pH 8.5)
Divalents: 0.3 M Magnesium chloride hexahydrate, 0.3 M Calcium chloride dihydrate
Crystal Properties Matthews coefficient Solvent content 1.93 36.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.646 α = 90 b = 31.599 β = 100.2 c = 127.006 γ = 90
Symmetry Space Group I 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 2021-06-21 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 1.6 40.08 96.29 0.0539 0.0642 0.0344 0.998 12.68 3.4 23048 26.15
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 1.6 1.67 94.55 0.7828 0.9433 0.5167 0.627 1.49
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 1.6 40.08 1.34 23048 1177 96.29 0.1717 0.1706 0.1704 0.1905 0.1905 35.22
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 13.8061 f_angle_d 1.0693 f_chiral_restr 0.0557 f_plane_restr 0.0137 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1552 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing