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Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2N8O 2N8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 292 A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.2 M ammonium sulphate, 0.1 M sodium acetate and 24.5% PEG 4000 v/v precipitant condition, pH 5.6 in a 1 microlitre sitting drop. Crystals were submerged in 20% PEG 400 in the precipitant solution as cryoprotectant and flash frozen in liquid nitrogen during harvesting.
Crystal Properties Matthews coefficient Solvent content 2.93 58.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.74 α = 90 b = 36.58 β = 95.98 c = 106.15 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M-F 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9119 Diamond I04-1
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 36.2 86 0.995 9.7 3 89417
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 1.15 38.7 0.787 1.4 1.2
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 2N8O 1.13 36.198 89417 4466 85.703 0.184 0.1825 0.1865 0.209 0.2127 14.71
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] 0.141 0.619 -0.495 0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.892 r_dihedral_angle_3_deg 13.431 r_dihedral_angle_1_deg 4.945 r_lrange_other 2.339 r_lrange_it 2.338 r_scangle_it 1.787 r_scangle_other 1.77 r_scbond_it 1.442 r_scbond_other 1.432 r_angle_refined_deg 1.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.892 r_dihedral_angle_3_deg 13.431 r_dihedral_angle_1_deg 4.945 r_lrange_other 2.339 r_lrange_it 2.338 r_scangle_it 1.787 r_scangle_other 1.77 r_scbond_it 1.442 r_scbond_other 1.432 r_angle_refined_deg 1.404 r_mcangle_it 1.158 r_mcangle_other 1.157 r_angle_other_deg 1.128 r_rigid_bond_restr 1.028 r_mcbond_it 0.895 r_mcbond_other 0.894 r_nbd_other 0.304 r_symmetry_nbd_refined 0.273 r_nbd_refined 0.226 r_nbtor_refined 0.211 r_symmetry_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.143 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1704 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing Coot model building