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Structure of the crosslinked PCP-E didomain of tyrocidine synthetase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ISX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 295 50 mM MES, 1.8 M ammonium sulfate, 10% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 3.21 61.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.381 α = 90 b = 216.381 β = 90 c = 59.758 γ = 120
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 PILATUS3 2M 2023-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 2.18 46.85 100 0.13 0.144 0.062 0.998 13.6 10.3 83879
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 2.18 2.22 100 1.401 1.558 0.674 0.691 1.8 10.2
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 FREE R-VALUE 2.18 46.85 83867 4242 99.983 0.19 0.1882 0.1876 0.2283 0.229 42.664
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] 0.586 0.293 0.586 -1.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.963 r_dihedral_angle_4_deg 18.073 r_dihedral_angle_3_deg 14.59 r_lrange_other 9.813 r_lrange_it 9.812 r_scangle_it 6.976 r_scangle_other 6.975 r_dihedral_angle_1_deg 6.786 r_mcangle_it 5.055 r_mcangle_other 5.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.963 r_dihedral_angle_4_deg 18.073 r_dihedral_angle_3_deg 14.59 r_lrange_other 9.813 r_lrange_it 9.812 r_scangle_it 6.976 r_scangle_other 6.975 r_dihedral_angle_1_deg 6.786 r_mcangle_it 5.055 r_mcangle_other 5.055 r_scbond_it 4.669 r_scbond_other 4.668 r_mcbond_it 3.549 r_mcbond_other 3.547 r_angle_refined_deg 1.553 r_angle_other_deg 1.343 r_symmetry_nbd_refined 0.385 r_symmetry_xyhbond_nbd_refined 0.29 r_nbd_other 0.236 r_nbd_refined 0.205 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8507 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 166
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement