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Lytic Transglycosylase MltD of Pseudomonas aeruginosa in a ternary complex bound to Bulgecin A and chito-tetraose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.1 M MES pH 6.5, 25% w/v PEG 550 MME, and 10 mM zinc sulfate
Crystal Properties Matthews coefficient Solvent content 2.06 40.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.248 α = 90 b = 117.036 β = 90 c = 120.146 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 2022-03-20 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) 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 1.98 83.84 87.8 0.9992 16.72 13.13 47136
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 96.2 0.6743 1.696
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.98 83.835 45208 2232 99.634 0.191 0.1902 0.1966 0.2155 0.2214 49.644
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] 1.081 -0.478 -0.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.908 r_dihedral_angle_3_deg 14.229 r_lrange_it 6.986 r_lrange_other 6.975 r_dihedral_angle_1_deg 5.778 r_dihedral_angle_2_deg 5.231 r_scangle_it 4.604 r_scangle_other 4.603 r_mcangle_it 3.717 r_mcangle_other 3.716
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.908 r_dihedral_angle_3_deg 14.229 r_lrange_it 6.986 r_lrange_other 6.975 r_dihedral_angle_1_deg 5.778 r_dihedral_angle_2_deg 5.231 r_scangle_it 4.604 r_scangle_other 4.603 r_mcangle_it 3.717 r_mcangle_other 3.716 r_scbond_it 2.788 r_scbond_other 2.785 r_mcbond_it 2.248 r_mcbond_other 2.248 r_dihedral_angle_other_2_deg 2.188 r_angle_refined_deg 1.026 r_angle_other_deg 0.364 r_nbd_refined 0.216 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.159 r_nbd_other 0.159 r_symmetry_xyhbond_nbd_refined 0.141 r_symmetry_nbd_refined 0.132 r_ncsr_local_group_1 0.119 r_metal_ion_refined 0.108 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4423 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing