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Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannobiose
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 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.296 α = 90 b = 43.734 β = 96.87 c = 85.407 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 2016-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 60.86 91.6 0.16 4.6 2.9 24135
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 2.1 2.16 57.2 0.84 0.55 1.4 2.6
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 2.1 60.86 22849 1226 90.96 0.19452 0.19181 0.2032 0.24698 0.2588 RANDOM 27.622
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] 3.02 -0.29 -2.22 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.883 r_dihedral_angle_4_deg 13.831 r_dihedral_angle_3_deg 13.504 r_dihedral_angle_1_deg 6.248 r_long_range_B_refined 3.229 r_long_range_B_other 3.229 r_scangle_other 2.218 r_mcangle_it 1.847 r_mcangle_other 1.847 r_scbond_it 1.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.883 r_dihedral_angle_4_deg 13.831 r_dihedral_angle_3_deg 13.504 r_dihedral_angle_1_deg 6.248 r_long_range_B_refined 3.229 r_long_range_B_other 3.229 r_scangle_other 2.218 r_mcangle_it 1.847 r_mcangle_other 1.847 r_scbond_it 1.356 r_scbond_other 1.356 r_angle_refined_deg 1.284 r_mcbond_it 1.164 r_mcbond_other 1.163 r_angle_other_deg 0.929 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3478 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling