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UDPG-bound Trehalose transferase 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 6.5 292 Bis-Tris Propane, PEG 3350, potassium thiocyanate, PEG 400
Crystal Properties Matthews coefficient Solvent content 2.02 39.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.045 α = 90 b = 69.327 β = 90 c = 98.912 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 2019-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976200 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 1.9 98.9 99.3 0.065 0.077 0.041 0.999 14.6 6.5 29213 39.056
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 1.9 1.94 98.5 1.337 1.58 0.836 0.508 1.3 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 (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 1.9 56.771 29172 1445 99.036 0.187 0.1847 0.1911 0.2227 0.2281 39.5
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] 1.214 -1.036 -0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.086 r_dihedral_angle_4_deg 17.693 r_dihedral_angle_3_deg 13.001 r_lrange_it 6.53 r_lrange_other 6.519 r_dihedral_angle_1_deg 6.501 r_scangle_it 4.97 r_scangle_other 4.969 r_mcangle_it 3.418 r_mcangle_other 3.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.086 r_dihedral_angle_4_deg 17.693 r_dihedral_angle_3_deg 13.001 r_lrange_it 6.53 r_lrange_other 6.519 r_dihedral_angle_1_deg 6.501 r_scangle_it 4.97 r_scangle_other 4.969 r_mcangle_it 3.418 r_mcangle_other 3.417 r_scbond_it 3.098 r_scbond_other 3.097 r_mcbond_it 2.35 r_mcbond_other 2.347 r_angle_refined_deg 1.351 r_angle_other_deg 1.267 r_symmetry_xyhbond_nbd_refined 0.247 r_nbd_other 0.212 r_nbd_refined 0.202 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.164 r_nbtor_refined 0.158 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.032 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3184 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing