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Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with beta-1,3-galactobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277 16% (w/v) PEG10000, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.32 46.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.608 α = 90 b = 97.954 β = 90 c = 161.252 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 100 CCD MARMOSAIC 225 mm CCD 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.1 50 99.9 0.2 0.223 0.083 10.624 7.1 27531
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.15 99.9 0.8 0.863 0.319 7.3
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 3W5G 3.1 43.43 26093 1375 99.9 0.201 0.199 0.2011 0.244 0.2423 RANDOM 41.31
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] -3.68 8.34 -4.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.455 r_dihedral_angle_4_deg 19.079 r_dihedral_angle_3_deg 16.779 r_long_range_B_refined 9.613 r_long_range_B_other 9.613 r_dihedral_angle_1_deg 7.583 r_scangle_other 4.391 r_mcangle_it 4.034 r_mcangle_other 4.033 r_scbond_it 2.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.455 r_dihedral_angle_4_deg 19.079 r_dihedral_angle_3_deg 16.779 r_long_range_B_refined 9.613 r_long_range_B_other 9.613 r_dihedral_angle_1_deg 7.583 r_scangle_other 4.391 r_mcangle_it 4.034 r_mcangle_other 4.033 r_scbond_it 2.628 r_scbond_other 2.628 r_mcbond_it 2.378 r_mcbond_other 2.378 r_angle_other_deg 2.302 r_angle_refined_deg 1.418 r_chiral_restr 0.067 r_bond_other_d 0.036 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 11054 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building