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Structure of racemic Ala-(8,13,18) Magainin 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MAG PDB entry 2MAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Precipitant solution contained 0.1 M sodium citrate tribasic, pH 5.6, and 35% v/v tert-butanol. No additional cryoprotectant was necessary for vitrification of crystals in LN2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.38 α = 89.97 b = 53.459 β = 90.07 c = 29.75 γ = 89.98
Symmetry Space Group I -4 2 d
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2013-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 26.72 95.4 0.092 32.17 22.4 2247 26.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.79 64.3 0.374 3.9 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2MAG 1.75 26.69 2169 2169 95 95.42 0.1983 0.1965 0.2099 0.2328 0.2366 RANDOM 31.59
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] -0.63 -0.63 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.848 r_dihedral_angle_3_deg 16.79 r_dihedral_angle_1_deg 5.806 r_angle_refined_deg 2.43 r_angle_other_deg 1.189 r_chiral_restr 0.165 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 163 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose XPREP data reduction REFMAC refinement PDB_EXTRACT data extraction EMBL data collection DENZO data reduction SCALEPACK data scaling PHASER phasing