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Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of glycerol 3-phosphate
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 5.6 292 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 acetate, 0.2 M sodium citrate and 29% PEG 4000 v/v precipitant condition, pH 5.6 in a 1 microlitre sitting drop. The crystal was soaked with sn-glycerol-3-phosphate (334 mM in the precipitant solution) at 1:1 v/v for 24 hours (50 equivalents). 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 3.26 62.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.718 α = 90 b = 37.239 β = 92.973 c = 114.088 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 EIGER2 XE 16M 2020-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8153 Diamond I03
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 1.2 34.531 99.9 0.999 8.2 13.4 96953
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 1.2 1.22 99.6 0.88 1.3 13.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2N8O 1.2 34.531 96947 4912 99.866 0.177 0.176 0.2033 0.2409 19.865
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] -0.065 0.108 0.923 -0.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.925 r_dihedral_angle_3_deg 13.01 r_dihedral_angle_1_deg 4.816 r_lrange_it 3.326 r_lrange_other 3.053 r_scangle_it 3.032 r_scangle_other 3.031 r_rigid_bond_restr 2.818 r_scbond_it 2.717 r_scbond_other 2.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.925 r_dihedral_angle_3_deg 13.01 r_dihedral_angle_1_deg 4.816 r_lrange_it 3.326 r_lrange_other 3.053 r_scangle_it 3.032 r_scangle_other 3.031 r_rigid_bond_restr 2.818 r_scbond_it 2.717 r_scbond_other 2.626 r_mcangle_it 1.75 r_mcangle_other 1.749 r_angle_refined_deg 1.703 r_mcbond_other 1.638 r_mcbond_it 1.637 r_angle_other_deg 1.188 r_nbd_other 0.38 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.239 r_nbtor_refined 0.203 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_other 0.134 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.076 r_xyhbond_nbd_other 0.026 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 396 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing Coot model building