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Recognition of Staphylococcus aureus wall teichoic acid analogue TB87 (compound 3) by Fab4497
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D6C PDB entry 5D6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 10 mM MES-NaOH pH 6.2;
0.25 M sodium chloride;
20% (w/v) PEG 4000;
0.1 M Tris-HCl pH 8.5;
0.2 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3 58.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.033 α = 90 b = 112.915 β = 90 c = 154.993 γ = 90
Symmetry Space Group P 21 21 21
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 2019-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.84 46.98 100 0.085 0.1 0.054 0.999 11.6 6.6 98208 34.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.9 100 1.787 2.124 1.135 0.601 0.9 6.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE PDB entry 5D6C 1.84 46.004 97934 4988 99.76 0.19 0.1884 0.2179 0.2152 37.866
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] 0.747 1.315 -2.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.571 r_dihedral_angle_4_deg 20.242 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 7.71 r_lrange_it 7.23 r_lrange_other 7.126 r_scangle_it 5.668 r_scangle_other 5.61 r_scbond_it 3.776 r_mcangle_it 3.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.571 r_dihedral_angle_4_deg 20.242 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 7.71 r_lrange_it 7.23 r_lrange_other 7.126 r_scangle_it 5.668 r_scangle_other 5.61 r_scbond_it 3.776 r_mcangle_it 3.747 r_mcangle_other 3.747 r_scbond_other 3.727 r_mcbond_it 2.678 r_mcbond_other 2.673 r_angle_refined_deg 1.473 r_angle_other_deg 1.287 r_nbd_other 0.241 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.201 r_symmetry_nbd_other 0.18 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.116 r_ncsr_local_group_2 0.1 r_ncsr_local_group_1 0.079 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.059 r_symmetry_xyhbond_nbd_other 0.032 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6639 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing