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SH3-like cell wall binding domain of the GH24 family muramidase from Trichophaea saccata in complex with triglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 10 mM triglycine added to the protein prior to crystallisation. Morpheus screen, condition D10
Crystal Properties Matthews coefficient Solvent content 1.83 32.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.105 α = 76.679 b = 27.234 β = 81.267 c = 50.039 γ = 72.662
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 EIGER2 XE 16M 2022-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.18 48.5 67 0.021 0.029 0.021 0.999 28.1 3.4 27938
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.2 4.7 0.145 0.206 0.145 0.977 3 1.3
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 8B2S 1.183 48.497 27928 1391 67.044 0.115 0.1131 0.1135 0.146 0.1456 12.994
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] -0.602 -0.013 -0.325 -0.094 -0.153 0.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.519 r_dihedral_angle_3_deg 9.331 r_dihedral_angle_1_deg 5.716 r_lrange_it 3.36 r_rigid_bond_restr 3.239 r_dihedral_angle_2_deg 2.966 r_lrange_other 2.933 r_scangle_it 2.737 r_scangle_other 2.735 r_scbond_other 2.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.519 r_dihedral_angle_3_deg 9.331 r_dihedral_angle_1_deg 5.716 r_lrange_it 3.36 r_rigid_bond_restr 3.239 r_dihedral_angle_2_deg 2.966 r_lrange_other 2.933 r_scangle_it 2.737 r_scangle_other 2.735 r_scbond_other 2.508 r_scbond_it 2.492 r_mcangle_it 2.368 r_mcangle_other 2.366 r_mcbond_it 1.72 r_mcbond_other 1.72 r_angle_refined_deg 1.396 r_angle_other_deg 0.498 r_xyhbond_nbd_refined 0.318 r_nbd_refined 0.222 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.179 r_nbd_other 0.169 r_symmetry_nbd_refined 0.147 r_ncsr_local_group_1 0.092 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.07 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1120 Nucleic Acid Atoms 26 Solvent Atoms 138 Heterogen Atoms 17
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement