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Structure-based mechanism of lipoteichoic acid synthesis by Staphylococcus aureus LtaS.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W5Q PDB ENTRY 2W5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 30% PEG4000, 100MM SODIUM CITRATE, PH5.6, 200MM AMMONIUM ACETATE, 30MG/ML GLYCEROL-PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.245 α = 90 b = 57.206 β = 90 c = 159.542 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 90 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 40.66 95.6 0.06 8.2 3.6 52534 2
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2W5Q 1.6 40.66 52534 2801 95.3 0.174 0.172 0.197 0.2109 RANDOM 14.55
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] 0.22 -0.02 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_4_deg 16.37 r_dihedral_angle_3_deg 11.58 r_dihedral_angle_1_deg 5.54 r_scangle_it 2.928 r_scbond_it 1.95 r_angle_refined_deg 1.219 r_mcangle_it 1.116 r_mcbond_it 0.689 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.21 r_dihedral_angle_4_deg 16.37 r_dihedral_angle_3_deg 11.58 r_dihedral_angle_1_deg 5.54 r_scangle_it 2.928 r_scbond_it 1.95 r_angle_refined_deg 1.219 r_mcangle_it 1.116 r_mcbond_it 0.689 r_nbtor_refined 0.312 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.083 r_symmetry_hbond_refined 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3450 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing