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Trehalose transferase (TreT) from Thermoproteus uzoniensis soaked with Mg
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 6.5 292 Bis-Tris Propane, PEG 3350, potassium thiocyanate, PEG 400
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.574 α = 90 b = 69.277 β = 90 c = 110.451 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-F 2019-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976300 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.15 110.45 98.8 0.07 0.081 0.039 0.999 17.1 7.8 25646
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 0.024 0.028 0.013 0.7 8.1
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 2.15 58.757 25646 1311 98.779 0.202 0.1985 0.1981 0.2612 0.2622 52.554
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] 3.601 -2.509 -1.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.393 r_dihedral_angle_4_deg 18.298 r_dihedral_angle_3_deg 14.688 r_lrange_other 7.814 r_lrange_it 7.808 r_dihedral_angle_1_deg 6.645 r_scangle_it 5.767 r_scangle_other 5.766 r_mcangle_it 4.927 r_mcangle_other 4.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.393 r_dihedral_angle_4_deg 18.298 r_dihedral_angle_3_deg 14.688 r_lrange_other 7.814 r_lrange_it 7.808 r_dihedral_angle_1_deg 6.645 r_scangle_it 5.767 r_scangle_other 5.766 r_mcangle_it 4.927 r_mcangle_other 4.926 r_scbond_it 3.54 r_scbond_other 3.539 r_mcbond_it 3.268 r_mcbond_other 3.262 r_angle_refined_deg 1.299 r_angle_other_deg 1.151 r_symmetry_nbd_refined 0.21 r_nbd_refined 0.195 r_symmetry_nbd_other 0.173 r_nbd_other 0.17 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.056 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 3162 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing