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Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannotriose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 200 mM MgCl2, 100 mM HEPES pH7.0, 27% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.414 α = 90 b = 44.016 β = 96.59 c = 85.079 γ = 90
Symmetry Space Group P 1 21 1
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-F 2016-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.980 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 51.82 99.8 0.035 1 21.8 4.1 263043
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 99.8 0.4 0.9 3.1 3.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.55 51.82 64689 3291 99.69 0.1487 0.147 0.1603 0.1801 0.1903 RANDOM 22.9027
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] 2.47 -0.19 -0.73 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.908 r_dihedral_angle_4_deg 17.234 r_dihedral_angle_3_deg 12.732 r_dihedral_angle_1_deg 6.345 r_angle_other_deg 3.65 r_mcangle_it 2.432 r_angle_refined_deg 2.067 r_mcbond_it 1.836 r_mcbond_other 1.836 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.908 r_dihedral_angle_4_deg 17.234 r_dihedral_angle_3_deg 12.732 r_dihedral_angle_1_deg 6.345 r_angle_other_deg 3.65 r_mcangle_it 2.432 r_angle_refined_deg 2.067 r_mcbond_it 1.836 r_mcbond_other 1.836 r_chiral_restr 0.128 r_gen_planes_other 0.026 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3479 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling