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Alpha-galactosidase from Thermotoga maritima in complex with hydrolysed cyclohexene-based carbasugar mimic of galactose
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 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.817 α = 90 b = 97.506 β = 90 c = 67.419 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 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 1.42 97.51 98.7 0.055 0.039 0.999 10.7 4.9 117828
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 1.42 1.46 93.9 0.948 0.742 0.493 1.5 3.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5M0X 1.42 68.44 111449 5853 98.08 0.17571 0.17434 0.1839 0.20158 0.2079 RANDOM 21.625
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] -0.79 -0.77 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.338 r_dihedral_angle_3_deg 12.872 r_dihedral_angle_4_deg 12.85 r_dihedral_angle_1_deg 7.151 r_long_range_B_other 5.952 r_long_range_B_refined 5.951 r_scangle_other 4.761 r_scbond_it 3.212 r_scbond_other 3.207 r_mcangle_other 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.338 r_dihedral_angle_3_deg 12.872 r_dihedral_angle_4_deg 12.85 r_dihedral_angle_1_deg 7.151 r_long_range_B_other 5.952 r_long_range_B_refined 5.951 r_scangle_other 4.761 r_scbond_it 3.212 r_scbond_other 3.207 r_mcangle_other 2.53 r_mcangle_it 2.529 r_mcbond_it 1.84 r_mcbond_other 1.836 r_angle_refined_deg 1.266 r_angle_other_deg 0.97 r_chiral_restr 0.072 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 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 4304 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing