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Alpha-galactosidase mutant D378A from Thermotoga maritima in complex with intact cyclohexene-based carbasugar mimic of galactose with 3,5 difluorophenyl leaving group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M MgSO4
20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.89 α = 90 b = 97.94 β = 90 c = 98.65 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M-F 2015-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 69.5 99.8 0.104 0.065 0.998 13.2 6.3 30612
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.5 0.737 0.518 0.737 2 5.4
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5M0X 2.2 69.5 29040 1521 99.69 0.17417 0.17088 0.23659 0.2018 RANDOM 36.197
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] 3.4 -3.66 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.761 r_dihedral_angle_4_deg 19.292 r_dihedral_angle_3_deg 15.787 r_dihedral_angle_1_deg 7.881 r_long_range_B_refined 7.111 r_long_range_B_other 7.111 r_scangle_other 5.864 r_mcangle_it 4.234 r_mcangle_other 4.234 r_scbond_it 3.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.761 r_dihedral_angle_4_deg 19.292 r_dihedral_angle_3_deg 15.787 r_dihedral_angle_1_deg 7.881 r_long_range_B_refined 7.111 r_long_range_B_other 7.111 r_scangle_other 5.864 r_mcangle_it 4.234 r_mcangle_other 4.234 r_scbond_it 3.872 r_scbond_other 3.872 r_mcbond_it 2.988 r_mcbond_other 2.987 r_angle_refined_deg 1.088 r_angle_other_deg 0.795 r_chiral_restr 0.054 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_gen_planes_other 0.001 r_bond_other_d 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 4256 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing