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Crystal structure of class III lanthipeptide synthetase LP-GS-ThurKC in complex with ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 282.15 0.2 M potassium citrate tribasic monohydrate and 19 % w/v PEG 3350, protein incubated at 18 mg/mL with 3mM ATP and 3mM Magnesium Chloride and soaked for 6 hours with 7 mM ATP and 7 mM Calcium Chloride
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.025 α = 90 b = 228.659 β = 100.504 c = 84.595 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 2021-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.00798 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 2.15 49.005 86.6 0.091 0.103 0.998 9.1 4.1 94386
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.157 82.6 1.372 1.555 0.376 0.9 4.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.15 49.005 94248 4665 86.441 0.205 0.203 0.2505 0.2439 60.008
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] -0.855 -0.701 3.844 -2.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.094 r_dihedral_angle_4_deg 19.509 r_dihedral_angle_3_deg 15.202 r_lrange_it 9.302 r_dihedral_angle_1_deg 6.808 r_scangle_it 6.668 r_mcangle_it 5.991 r_scbond_it 4.614 r_mcbond_it 3.969 r_angle_refined_deg 1.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.094 r_dihedral_angle_4_deg 19.509 r_dihedral_angle_3_deg 15.202 r_lrange_it 9.302 r_dihedral_angle_1_deg 6.808 r_scangle_it 6.668 r_mcangle_it 5.991 r_scbond_it 4.614 r_mcbond_it 3.969 r_angle_refined_deg 1.192 r_nbtor_refined 0.31 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.18 r_ncsr_local_group_1 0.131 r_chiral_restr 0.097 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13860 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling CRANK2 phasing