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Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the dimeric state
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 8.5 292 A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.7 M sodium citrate, 0.1 M Tris precipitant condition, pH 8.5 in a 0.4 microlitre sitting drop. Crystals were submerged in 2.0 M lithium sulphate as cryoprotectant and flash frozen in liquid nitrogen during harvesting.
Crystal Properties Matthews coefficient Solvent content 1.84 33.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.56 α = 90 b = 23.077 β = 114.351 c = 52.609 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 0.89 21.99 92.7 1 17.2 5.9 62368
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 0.89 0.91 46.4 0.831 1 3.5
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 0.89 21.99 62367 3106 92.749 0.195 0.1938 0.1973 0.2105 0.2141 11.304
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] -0.34 0.178 -0.317 0.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.568 r_dihedral_angle_3_deg 10.752 r_dihedral_angle_1_deg 5.178 r_lrange_it 2.631 r_lrange_other 2.63 r_rigid_bond_restr 1.909 r_scangle_it 1.814 r_scangle_other 1.813 r_angle_refined_deg 1.713 r_scbond_it 1.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.568 r_dihedral_angle_3_deg 10.752 r_dihedral_angle_1_deg 5.178 r_lrange_it 2.631 r_lrange_other 2.63 r_rigid_bond_restr 1.909 r_scangle_it 1.814 r_scangle_other 1.813 r_angle_refined_deg 1.713 r_scbond_it 1.563 r_scbond_other 1.561 r_mcangle_it 1.203 r_mcangle_other 1.202 r_angle_other_deg 1.168 r_mcbond_it 0.85 r_mcbond_other 0.845 r_nbd_other 0.277 r_symmetry_xyhbond_nbd_refined 0.248 r_xyhbond_nbd_refined 0.247 r_nbd_refined 0.243 r_symmetry_nbd_refined 0.243 r_symmetry_nbd_other 0.214 r_nbtor_refined 0.203 r_symmetry_xyhbond_nbd_other 0.182 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.081 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 852 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing Coot model building