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Lytic Transglycosylase MltD of Pseudomonas aeruginosa bound to the Natural Product Bulgecin A
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 1.94 36.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.224 α = 90 b = 113.408 β = 90 c = 116.858 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 2022-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 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 1.95 42.18 89.8 0.999 11.4 6 49604
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 1.95 1.99 0.4712 1.264
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 1.95 42.18 44670 2194 99.81 0.192 0.1905 0.1973 0.213 0.2195 44.818
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] -0.086 0.202 -0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.292 r_dihedral_angle_3_deg 15.123 r_lrange_it 6.817 r_lrange_other 6.785 r_dihedral_angle_2_deg 6.381 r_dihedral_angle_1_deg 5.687 r_scangle_it 4.133 r_scangle_other 4.133 r_mcangle_it 3.274 r_mcangle_other 3.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.292 r_dihedral_angle_3_deg 15.123 r_lrange_it 6.817 r_lrange_other 6.785 r_dihedral_angle_2_deg 6.381 r_dihedral_angle_1_deg 5.687 r_scangle_it 4.133 r_scangle_other 4.133 r_mcangle_it 3.274 r_mcangle_other 3.273 r_scbond_it 2.456 r_scbond_other 2.453 r_mcbond_it 2.013 r_mcbond_other 2.012 r_dihedral_angle_other_2_deg 1.866 r_angle_refined_deg 1.051 r_angle_other_deg 0.359 r_symmetry_nbd_refined 0.216 r_nbd_refined 0.215 r_nbd_other 0.197 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.135 r_ncsr_local_group_1 0.128 r_metal_ion_refined 0.118 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.054 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.004 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 4457 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing