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Trehalose transferase bound to alpha-D-glucopyranosyl-beta-galactopyranose from Thermoproteus uzoniensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other apo-Tret
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.6 292 Bis-Tris Propane, PEG 3350, potassium thiocyanide, PEG 400
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.01 α = 90 b = 68.771 β = 90 c = 110.868 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 PIXEL DECTRIS PILATUS 6M 2019-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97630 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 60 99.9 0.054 1 24.36 12.4 47789 34.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 99.94 1.568 0.69 1.47
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE apo-Tret 1.75 58.509 47789 2329 99.985 0.204 0.2021 0.2036 0.2345 0.2362 39.646
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] 1.109 -1.346 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.806 r_dihedral_angle_3_deg 13.953 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_1_deg 6.556 r_lrange_it 5.99 r_lrange_other 5.99 r_scangle_it 4.095 r_scangle_other 4.094 r_mcangle_it 3.628 r_mcangle_other 3.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.806 r_dihedral_angle_3_deg 13.953 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_1_deg 6.556 r_lrange_it 5.99 r_lrange_other 5.99 r_scangle_it 4.095 r_scangle_other 4.094 r_mcangle_it 3.628 r_mcangle_other 3.627 r_scbond_it 2.618 r_scbond_other 2.617 r_mcbond_it 2.39 r_mcbond_other 2.384 r_angle_refined_deg 1.309 r_angle_other_deg 1.202 r_nbd_other 0.3 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3210 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing