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Crystal structure of GH92 alpha-1,2-mannosidase from Enterococcus faecalis ATCC 10100 in complex with methyl alpha-1,2-C-mannobioside
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 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.162 α = 90 b = 169.601 β = 90 c = 258.659 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 2021-03-07 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 1.72 50 100 0.121 0.125 0.034 0.999 17.3 13.6 375878
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 1.72 1.81 100 1.168 1.214 0.327 0.759 2.5 13.5
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 6DWO 1.72 48.621 375801 18587 99.99 0.15 0.1489 0.1621 0.1714 0.1814 23.049
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] -0.029 -0.022 0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.079 r_dihedral_angle_4_deg 17.515 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_1_deg 6.889 r_lrange_it 5.832 r_lrange_other 5.704 r_scangle_it 4.84 r_scangle_other 4.84 r_scbond_it 3.278 r_scbond_other 3.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.079 r_dihedral_angle_4_deg 17.515 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_1_deg 6.889 r_lrange_it 5.832 r_lrange_other 5.704 r_scangle_it 4.84 r_scangle_other 4.84 r_scbond_it 3.278 r_scbond_other 3.278 r_mcangle_it 2.467 r_mcangle_other 2.467 r_mcbond_it 1.911 r_mcbond_other 1.911 r_angle_refined_deg 1.733 r_angle_other_deg 1.493 r_nbd_other 0.236 r_nbd_refined 0.207 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.169 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.069 r_metal_ion_refined 0.035 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 2760 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building