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The X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa
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 80mM Tris pH 8.5, 12% PEG 8000 and 160mM calcium acetate
Crystal Properties Matthews coefficient Solvent content 3.07 59.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.488 α = 90 b = 163.488 β = 90 c = 56.035 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 2017-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97953 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 3.05 141.58 99.88 0.048 11.94 11.7 16595
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 3.05 3.16 0.39
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 3.05 141.58 15785 810 99.9 0.18468 0.18146 0.1851 0.24967 0.247 RANDOM 82.949
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] 0.7 0.35 0.7 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.794 r_dihedral_angle_4_deg 18.657 r_dihedral_angle_3_deg 17.193 r_long_range_B_refined 6.699 r_long_range_B_other 6.698 r_dihedral_angle_1_deg 6.016 r_mcangle_it 4.264 r_mcangle_other 4.263 r_scangle_other 4.124 r_mcbond_it 2.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.794 r_dihedral_angle_4_deg 18.657 r_dihedral_angle_3_deg 17.193 r_long_range_B_refined 6.699 r_long_range_B_other 6.698 r_dihedral_angle_1_deg 6.016 r_mcangle_it 4.264 r_mcangle_other 4.263 r_scangle_other 4.124 r_mcbond_it 2.559 r_mcbond_other 2.557 r_scbond_it 2.38 r_scbond_other 2.379 r_angle_refined_deg 1.206 r_angle_other_deg 0.931 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 4980 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing