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Crystal structure of the mutant E494Q of GH92 alpha-1,2-mannosidase from Enterococcus faecalis ATCC 10100 in complex with alpha-1,2-mannobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DWO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM sodium citrate, pH 5.0-5.6, 100 mM magnesium acetate, 200 mM ammonium sulfate, 5% PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.626 α = 90 b = 168.61 β = 90 c = 260.282 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 S 2M 2021-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.75 50 99.6 0.141 0.147 0.04 0.998 12.2 13.3 354371
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 1.75 1.84 99.1 1.254 1.305 0.361 0.681 2.1 12.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6DWO 1.75 48.566 354296 17508 99.555 0.17 0.1686 0.1979 0.1892 26
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] -0.506 -0.339 0.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 16.879 r_dihedral_angle_3_deg 14.244 r_dihedral_angle_1_deg 7.043 r_lrange_it 5.675 r_lrange_other 5.632 r_scangle_it 4.295 r_scangle_other 4.295 r_mcangle_it 2.968 r_mcangle_other 2.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 16.879 r_dihedral_angle_3_deg 14.244 r_dihedral_angle_1_deg 7.043 r_lrange_it 5.675 r_lrange_other 5.632 r_scangle_it 4.295 r_scangle_other 4.295 r_mcangle_it 2.968 r_mcangle_other 2.968 r_scbond_it 2.854 r_scbond_other 2.854 r_mcbond_it 2.084 r_mcbond_other 2.084 r_angle_refined_deg 1.612 r_angle_other_deg 1.411 r_nbd_refined 0.203 r_nbd_other 0.186 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.169 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.116 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.078 r_symmetry_xyhbond_nbd_other 0.015 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23052 Nucleic Acid Atoms Solvent Atoms 1773 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building