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Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose covalently linked to the nucleophile
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
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.73 α = 90 b = 95.87 β = 90 c = 97.44 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 2017-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.77 24.36 99.9 0.118 0.074 0.997 9 6.6 61617
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 1.77 1.82 56.4 1.438 0.903 0.564 1.1 6.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5M0X 1.77 24.36 58648 2901 99.91 0.16969 0.16738 0.1781 0.21495 0.2207 RANDOM 27.819
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] 2.38 -1.69 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.647 r_dihedral_angle_4_deg 20.99 r_dihedral_angle_3_deg 14.942 r_dihedral_angle_1_deg 7.467 r_long_range_B_refined 6.811 r_long_range_B_other 6.81 r_scangle_other 5.475 r_scbond_it 3.834 r_scbond_other 3.834 r_mcangle_it 3.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.647 r_dihedral_angle_4_deg 20.99 r_dihedral_angle_3_deg 14.942 r_dihedral_angle_1_deg 7.467 r_long_range_B_refined 6.811 r_long_range_B_other 6.81 r_scangle_other 5.475 r_scbond_it 3.834 r_scbond_other 3.834 r_mcangle_it 3.384 r_mcangle_other 3.383 r_mcbond_it 2.629 r_mcbond_other 2.626 r_angle_refined_deg 1.207 r_angle_other_deg 0.915 r_chiral_restr 0.071 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 r_bond_other_d 0.001 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 4276 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing