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Muramidase from Thermothielavioides terrestris, catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PACT screen condition D12 (0.01 M zinc chloride, 0.1 M Tris pH 8, 20% w/v PEG 6000)
Crystal Properties Matthews coefficient Solvent content 3.07 59.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.616 α = 90 b = 84.616 β = 90 c = 62.882 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 CCD ADSC QUANTUM 315 2018-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 2.36 36.64 99.9 0.123 0.133 0.051 0.999 12.1 12.5 10659 47.4
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 2.36 2.45 99.7 1.215 1.319 0.505 0.87 1.6 12.9
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 8B2E 2.36 36.64 10645 492 99.906 0.198 0.1971 0.2038 0.2207 0.2266 63.097
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] 2.569 1.285 2.569 -8.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.665 r_dihedral_angle_3_deg 14.175 r_lrange_it 6.365 r_lrange_other 6.352 r_dihedral_angle_2_deg 5.422 r_dihedral_angle_1_deg 5.295 r_scangle_it 4.861 r_scangle_other 4.858 r_mcangle_it 4.284 r_mcangle_other 4.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.665 r_dihedral_angle_3_deg 14.175 r_lrange_it 6.365 r_lrange_other 6.352 r_dihedral_angle_2_deg 5.422 r_dihedral_angle_1_deg 5.295 r_scangle_it 4.861 r_scangle_other 4.858 r_mcangle_it 4.284 r_mcangle_other 4.281 r_scbond_it 3.383 r_scbond_other 3.231 r_mcbond_it 2.869 r_mcbond_other 2.865 r_angle_refined_deg 0.972 r_angle_other_deg 0.307 r_nbd_refined 0.223 r_symmetry_nbd_other 0.184 r_nbd_other 0.175 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.124 r_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.071 r_metal_ion_refined 0.048 r_symmetry_metal_ion_refined 0.048 r_chiral_restr 0.044 r_symmetry_xyhbond_nbd_other 0.038 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 1052 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 6
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement