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Atomic resolution crystal structure of the hexameric antimicrobial peptide Magainin-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 35% MPD, 20 mM HEPES, pH 7
Crystal Properties Matthews coefficient Solvent content 1.92 36.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.359 α = 90 b = 34.359 β = 90 c = 55.795 γ = 120
Symmetry Space Group P 63 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 PILATUS 6M 2017-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.05 29.76 97.81 0.029 0.99 27.36 8.1 9455
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 1.05 1.077 0.92 0.51 4.35
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 1.05 29.756 9455 946 97.807 0.168 0.1674 0.1766 0.177 0.1886 22.402
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] -0.035 -0.017 -0.035 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.358 r_dihedral_angle_6_deg 10.873 r_rigid_bond_restr 5.667 r_lrange_it 5.02 r_lrange_other 5.002 r_scangle_it 3.189 r_scangle_other 3.178 r_mcangle_it 2.5 r_dihedral_angle_1_deg 2.448 r_scbond_it 2.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.358 r_dihedral_angle_6_deg 10.873 r_rigid_bond_restr 5.667 r_lrange_it 5.02 r_lrange_other 5.002 r_scangle_it 3.189 r_scangle_other 3.178 r_mcangle_it 2.5 r_dihedral_angle_1_deg 2.448 r_scbond_it 2.329 r_scbond_other 2.32 r_mcangle_other 2.172 r_mcbond_it 1.756 r_mcbond_other 1.755 r_angle_refined_deg 1.553 r_angle_other_deg 0.515 r_nbd_other 0.322 r_symmetry_nbd_refined 0.29 r_symmetry_xyhbond_nbd_refined 0.287 r_nbd_refined 0.243 r_nbtor_refined 0.21 r_symmetry_nbd_other 0.169 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.065 r_xyhbond_nbd_refined 0.022 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 168 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling BUCCANEER phasing