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Reversible supramolecular assembly of the anti-microbial peptide plectasin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 300 15 mg/mL plectasin in 10 mM His pH 4.5 added to a reservoir of 0.1 M NH4Ac, 0.1 M Tris pH 8.5 and 40% isopropanol
Crystal Properties Matthews coefficient Solvent content 1.7 27.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.678 α = 90 b = 20.093 β = 104.279 c = 32.546 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 16M Kirkpatrick-Baez (KB) mirror pair (VFM, HFM) 2020-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97247 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.13 31.53 89.9 0.999 22.49 6 10216
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.2 0.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3E7U 1.131 21.219 10215 507 90.231 0.147 0.1457 0.1432 0.1781 0.1786 27.922
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] 2.945 1.224 -2.283 -1.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.955 r_dihedral_angle_3_deg 22.952 r_lrange_it 7.751 r_scangle_it 7.73 r_scangle_other 7.495 r_scbond_it 7.27 r_scbond_other 7.005 r_lrange_other 6.994 r_rigid_bond_restr 6.438 r_dihedral_angle_1_deg 4.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.955 r_dihedral_angle_3_deg 22.952 r_lrange_it 7.751 r_scangle_it 7.73 r_scangle_other 7.495 r_scbond_it 7.27 r_scbond_other 7.005 r_lrange_other 6.994 r_rigid_bond_restr 6.438 r_dihedral_angle_1_deg 4.441 r_mcangle_it 3.414 r_mcangle_other 3.406 r_mcbond_other 2.671 r_mcbond_it 2.667 r_angle_refined_deg 1.965 r_angle_other_deg 0.686 r_symmetry_nbd_refined 0.261 r_nbd_other 0.255 r_nbd_refined 0.252 r_symmetry_nbd_other 0.244 r_nbtor_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.177 r_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.098 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 305 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing