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Crystal structure of the human LL37(17-29) I24C mutant antimicrobial peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S6M PDBid 6S6M with residues mutated to alanine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 The LL-37(17-29) I24C peptide was mixed with 0.1mM DTT in water: Reservoir contained 2.8 M sodium acetate trihydrate pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.98 37.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.92 α = 90 b = 34.92 β = 90 c = 44.57 γ = 90
Symmetry Space Group P 41 21 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 EIGER X 16M 2019-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.5 27.49 99 0.052 0.056 0.999 19.87 7.571 4721 29.339
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 1.5 1.55 91 0.658 0.751 0.699 2.17 3.773
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDBid 6S6M with residues mutated to alanine 1.5 27.49 4249 472 99.04 0.1803 0.1789 0.1917 0.213 RANDOM 28.058
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] 0.29 0.29 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.507 r_dihedral_angle_4_deg 21.453 r_dihedral_angle_3_deg 16.69 r_dihedral_angle_1_deg 4.171 r_angle_refined_deg 1.946 r_angle_other_deg 1.484 r_chiral_restr 0.116 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.507 r_dihedral_angle_4_deg 21.453 r_dihedral_angle_3_deg 16.69 r_dihedral_angle_1_deg 4.171 r_angle_refined_deg 1.946 r_angle_other_deg 1.484 r_chiral_restr 0.116 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 240 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction