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Crystal structure of class III lanthipeptide synthetase ThurKC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SAM model used for molecular replacement was obtained in the same body of work
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 282.15 18% (w/v) PEG 3350, 100 mM Bis tris propane/ hydrochloric acid pH 7.5, 200 mM sodium fluoride, and 3% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.75 55.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.296 α = 90 b = 230.23 β = 100.617 c = 84.383 γ = 90
Symmetry Space Group P 1 21 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 9M 2020-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12706 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.52 115.115 98.9 0.067 0.075 0.998 12.4 4.7 68899
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.528 0.824 0.829 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.52 115.115 68899 3422 98.889 0.192 0.1892 0.1905 0.2503 0.2524 87.984
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] 3.056 -1.312 3.1 -5.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.94 r_dihedral_angle_4_deg 20.298 r_dihedral_angle_3_deg 17.603 r_lrange_it 14.335 r_scangle_it 9.95 r_mcangle_it 9.332 r_dihedral_angle_1_deg 7.092 r_scbond_it 6.66 r_mcbond_it 6.131 r_angle_refined_deg 1.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.94 r_dihedral_angle_4_deg 20.298 r_dihedral_angle_3_deg 17.603 r_lrange_it 14.335 r_scangle_it 9.95 r_mcangle_it 9.332 r_dihedral_angle_1_deg 7.092 r_scbond_it 6.66 r_mcbond_it 6.131 r_angle_refined_deg 1.239 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.202 r_ncsr_local_group_1 0.148 r_symmetry_xyhbond_nbd_refined 0.124 r_chiral_restr 0.109 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13522 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling CRANK2 phasing