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Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with a hydrolysed cyclopropyl carbasugar.
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 magnesium sulfate, 20% (w/v) PEG 3350
Crystals were soaked for 7 days in 1 mM inhibitor, 30% (w/v) PEG 3350 before freezing.
Crystal Properties Matthews coefficient Solvent content 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.3 α = 90 b = 96.02 β = 90 c = 98.05 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 2M 2014-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 Diamond I04-1
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 1.62 55.66 99.6 0.055 15.8 5.1 82206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.66 99.7 0.594 2.4 4.6
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 1.62 55.66 78077 4059 99.5 0.17351 0.1722 0.19788 0.1926 RANDOM 24.183
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] 3.26 -1.45 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.611 r_dihedral_angle_4_deg 18.64 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 6.975 r_long_range_B_refined 5.989 r_long_range_B_other 5.988 r_scangle_other 5.195 r_scbond_it 3.668 r_scbond_other 3.668 r_mcangle_it 3.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.611 r_dihedral_angle_4_deg 18.64 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 6.975 r_long_range_B_refined 5.989 r_long_range_B_other 5.988 r_scangle_other 5.195 r_scbond_it 3.668 r_scbond_other 3.668 r_mcangle_it 3.016 r_mcangle_other 3.016 r_mcbond_it 2.333 r_mcbond_other 2.331 r_angle_refined_deg 1.607 r_angle_other_deg 0.847 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 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 4316 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing Coot model building