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Recognition of Staphylococcus aureus wall teichoic acid analogue SA533 (compound 1) by Fab4461
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I1D separate constant and variable domains of PDB entry 5I1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 294 10 mM Tris-HCl;
250 mM sodium chloride;
12.9 % w/v polyethylene glycol 20,000;
150 mM CAPSO pH 9.5;
6 % v/v polyethylene glycol 300
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.191 α = 90 b = 65.448 β = 112.899 c = 74.338 γ = 90
Symmetry Space Group P 1 21 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 2020-12-01 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 1.45 53.51 96.6 0.028 0.039 0.027 0.997 16.4 3.1 87656 21.8
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 1.45 1.53 80.6 0.43 0.593 0.406 0.608 1.5 2.5
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 separate constant and variable domains of PDB entry 5I1D 1.452 53.51 87588 4368 96.54 0.176 0.1743 0.1741 0.1999 0.1996 23.016
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] -0.415 -0.061 0.101 0.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.742 r_dihedral_angle_4_deg 21.132 r_dihedral_angle_3_deg 11.908 r_dihedral_angle_1_deg 7.152 r_lrange_it 6.356 r_lrange_other 6.302 r_scangle_it 4.08 r_scangle_other 4.079 r_mcangle_it 3.201 r_mcangle_other 3.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.742 r_dihedral_angle_4_deg 21.132 r_dihedral_angle_3_deg 11.908 r_dihedral_angle_1_deg 7.152 r_lrange_it 6.356 r_lrange_other 6.302 r_scangle_it 4.08 r_scangle_other 4.079 r_mcangle_it 3.201 r_mcangle_other 3.2 r_scbond_it 2.613 r_scbond_other 2.613 r_mcbond_it 1.943 r_mcbond_other 1.94 r_angle_refined_deg 1.498 r_angle_other_deg 1.352 r_symmetry_nbd_refined 0.237 r_symmetry_xyhbond_nbd_refined 0.231 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.197 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.163 r_nbd_other 0.121 r_xyhbond_nbd_other 0.084 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.048 r_chiral_restr_other 0.029 r_bond_refined_d 0.009 r_gen_planes_refined 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 3317 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing