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Structure of quasiracemic Ala-Magainin 2 with a beta amino acid substitution at position 13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-butanol
Crystal Properties Matthews coefficient Solvent content 1.78 30.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.85 α = 109.76 b = 27 β = 102.35 c = 29.96 γ = 90.23
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 2013-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 27.45 96.1 0.052 14.94 3.75 10964
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 1.5 1.6 94.4 0.31 5.02 3.75
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4MGP 1.5 27.45 10395 566 96.1 0.17462 0.17166 0.1731 0.23889 0.2396 RANDOM 27.15
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] -2.01 -0.54 0.02 -1.14 1.1 1.67
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 50.239 r_dihedral_angle_2_deg 33.648 r_dihedral_angle_3_deg 14.908 r_dihedral_angle_1_deg 13.184 r_sphericity_bonded 8.825 r_long_range_B_refined 4.253 r_long_range_B_other 3.317 r_scangle_other 2.716 r_scbond_other 2.508 r_scbond_it 2.505
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 50.239 r_dihedral_angle_2_deg 33.648 r_dihedral_angle_3_deg 14.908 r_dihedral_angle_1_deg 13.184 r_sphericity_bonded 8.825 r_long_range_B_refined 4.253 r_long_range_B_other 3.317 r_scangle_other 2.716 r_scbond_other 2.508 r_scbond_it 2.505 r_mcangle_other 2.379 r_mcangle_it 2.367 r_mcbond_it 1.98 r_mcbond_other 1.952 r_angle_refined_deg 1.773 r_rigid_bond_restr 1.205 r_angle_other_deg 1.025 r_chiral_restr 0.095 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 690 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing