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The X-ray Structure of Lytic Transglycosylase Slt from Pseudomonas aeruginosa in complex with the reaction product NAG-anhNAMpentapeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.4M sodium potassium phosphate pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.526 α = 90 b = 165.526 β = 90 c = 54.733 γ = 120
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 2016-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97919 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.5 143.35 99.93 0.024 15.2 15.2 30002
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 0.36
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5OHU 2.5 143.35 28541 1457 99.93 0.18298 0.18002 0.1847 0.23944 0.2457 RANDOM 67.247
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] -1.79 -0.9 -1.79 5.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.616 r_dihedral_angle_4_deg 18.245 r_dihedral_angle_3_deg 17.682 r_long_range_B_other 11.328 r_long_range_B_refined 11.327 r_scangle_other 8.652 r_mcangle_it 7.578 r_mcangle_other 7.577 r_dihedral_angle_1_deg 6.421 r_scbond_it 5.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.616 r_dihedral_angle_4_deg 18.245 r_dihedral_angle_3_deg 17.682 r_long_range_B_other 11.328 r_long_range_B_refined 11.327 r_scangle_other 8.652 r_mcangle_it 7.578 r_mcangle_other 7.577 r_dihedral_angle_1_deg 6.421 r_scbond_it 5.848 r_scbond_other 5.847 r_mcbond_it 5.124 r_mcbond_other 5.123 r_angle_refined_deg 1.673 r_angle_other_deg 1.072 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5013 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing