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apo-Trehalose transferase (apo-TreT) from Thermoproteus uzoniensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X6Q
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 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.519 α = 90 b = 68.776 β = 90 c = 112.2 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 2019-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976250 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 2.1 68.78 96.8 0.065 0.084 0.053 0.997 8.5 3.6 27351
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 2.1 2.16 93.6 0.73 0.98 0.648 0.45 2.9
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 2x6q 2.1 58.705 27320 1336 95.88 0.197 0.208 0.1926 0.255 0.2556 47.711
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] 1.979 -1.053 -0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.471 r_dihedral_angle_4_deg 20.026 r_dihedral_angle_3_deg 14.491 r_lrange_it 8.14 r_lrange_other 8.132 r_dihedral_angle_1_deg 6.479 r_scangle_it 6.254 r_scangle_other 6.221 r_mcangle_it 5.098 r_mcangle_other 5.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.471 r_dihedral_angle_4_deg 20.026 r_dihedral_angle_3_deg 14.491 r_lrange_it 8.14 r_lrange_other 8.132 r_dihedral_angle_1_deg 6.479 r_scangle_it 6.254 r_scangle_other 6.221 r_mcangle_it 5.098 r_mcangle_other 5.097 r_scbond_it 4.087 r_scbond_other 4.047 r_mcbond_it 3.525 r_mcbond_other 3.518 r_angle_refined_deg 1.446 r_angle_other_deg 1.242 r_nbd_refined 0.198 r_symmetry_nbd_other 0.19 r_nbd_other 0.165 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.162 r_nbtor_refined 0.16 r_symmetry_nbd_refined 0.128 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3185 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing