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Crystal structure of lasso peptide epimerase MslH in complexed with precursor peptide variant MslAW21G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 200 mM magnesium chloride, 100 mM Tris-HCl (pH 9.0), 34% (w/v) PEG400
Crystal Properties Matthews coefficient Solvent content 3.33 63.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.232 α = 90 b = 127.232 β = 90 c = 170.611 γ = 90
Symmetry Space Group I 4 2 2
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 4M 2023-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.03500 Photon Factory BL-1A
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 2.12 45.18 100 0.08 0.092 0.046 0.999 18.7 7.6 40284 42.42
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 2.12 2.18 100 0.821 0.947 0.466 0.81 2.3 7.9
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 2.25 44.98 1.34 33441 1995 99.79 0.1837 0.1822 0.1837 0.2068 0.2076 52.76
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 22.9891 f_angle_d 0.5422 f_chiral_restr 0.0419 f_plane_restr 0.0043 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3352 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing