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X-ray structure of the lytic transglycosylase SltB2 from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ANZ 5ANZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 20% Polyethylene Glycol 4000, 0.1 M sodium acetate and 8% 2-propanol
Crystal Properties Matthews coefficient Solvent content 1.89 35.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.966 α = 90 b = 42.395 β = 95.646 c = 93.579 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 2018-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 46.56 99 0.086 0.036 0.998 13 6.6 36814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.3 1.072 0.435 0.698 2.3 6.9
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 5ANZ 1.7 46.56 36801 1778 98.84 0.165 0.1639 0.1747 0.1953 0.2058 24.924
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] 0.505 1.45 -0.517 -0.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.849 r_dihedral_angle_4_deg 15.223 r_dihedral_angle_3_deg 13.221 r_dihedral_angle_1_deg 6.038 r_lrange_it 5.569 r_lrange_other 5.238 r_scangle_it 3.246 r_scangle_other 3.245 r_mcangle_it 2.187 r_mcangle_other 2.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.849 r_dihedral_angle_4_deg 15.223 r_dihedral_angle_3_deg 13.221 r_dihedral_angle_1_deg 6.038 r_lrange_it 5.569 r_lrange_other 5.238 r_scangle_it 3.246 r_scangle_other 3.245 r_mcangle_it 2.187 r_mcangle_other 2.187 r_scbond_it 2 r_scbond_other 1.999 r_angle_refined_deg 1.467 r_angle_other_deg 1.453 r_mcbond_it 1.36 r_mcbond_other 1.352 r_xyhbond_nbd_other 0.315 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_other 0.214 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.189 r_symmetry_nbd_refined 0.186 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.167 r_metal_ion_refined 0.134 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.071 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 2886 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing