☰ Navigation Tabs
Recognition of Staphylococcus aureus wall teichoic acid analogue SA475 (compound 2) 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 294 10 mM 2-(N-morpholino)ethanesulfonic acid-NaOH pH 6.2,
0.25 M sodium chloride,
20% (w/v) poly-ethylene glycol 4000,
10% (v/v) glycerol,
200 mM magnesium sulphate
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.392 α = 90 b = 113.371 β = 90 c = 154.557 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 2020-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97933 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 1.649 91.41 92.9 0.077 0.092 0.049 0.998 12 6.5 127285 24.4
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 1.649 1.74 100 1.047 1.247 0.67 0.661 1.5 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE PDB entry 5D6C 1.649 90.016 127097 6287 92.962 0.176 0.1747 0.1857 0.2018 0.2102 25.699
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 -0.59 -0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.184 r_dihedral_angle_4_deg 22.83 r_dihedral_angle_3_deg 13.049 r_dihedral_angle_1_deg 7.67 r_lrange_it 6.64 r_lrange_other 6.503 r_scangle_it 4.859 r_scangle_other 4.832 r_mcangle_it 3.239 r_mcangle_other 3.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.184 r_dihedral_angle_4_deg 22.83 r_dihedral_angle_3_deg 13.049 r_dihedral_angle_1_deg 7.67 r_lrange_it 6.64 r_lrange_other 6.503 r_scangle_it 4.859 r_scangle_other 4.832 r_mcangle_it 3.239 r_mcangle_other 3.238 r_scbond_it 3.15 r_scbond_other 3.123 r_mcbond_it 2.166 r_mcbond_other 2.161 r_angle_refined_deg 1.548 r_angle_other_deg 1.394 r_symmetry_nbd_refined 0.231 r_symmetry_xyhbond_nbd_other 0.212 r_nbd_refined 0.196 r_symmetry_nbd_other 0.18 r_nbd_other 0.18 r_symmetry_xyhbond_nbd_refined 0.175 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.164 r_ncsr_local_group_1 0.092 r_ncsr_local_group_2 0.091 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.069 r_bond_refined_d 0.01 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 6636 Nucleic Acid Atoms Solvent Atoms 818 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing