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Crystal structures of trehalose synthase from Deinococcus radiodurans reveal that a closed conformation is involved in the intramolecular isomerization catalysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 288 11% PEG 4000, 0.2M sodium acetate trihydrate, 0.3M Tris-HCl (pH 8.5), 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.25 α = 90 b = 133.705 β = 90 c = 196.614 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 110 CCD ADSC QUANTUM 315r 2014-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 2.21 20 99.9 0.151 0.165 0.066 5.3 5.9 129348
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 2.21 2.29 99.7 0.787 0.862 0.345 0.784 5.6 12695
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4TVU 2.21 20 119863 6336 99.09 0.1621 0.1601 0.1996 0.1772 RANDOM 32.96
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] -0.03 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.115 r_dihedral_angle_4_deg 18.745 r_dihedral_angle_3_deg 14.979 r_dihedral_angle_1_deg 6.248 r_mcangle_it 2.576 r_mcbond_it 1.718 r_mcbond_other 1.717 r_angle_refined_deg 1.414 r_angle_other_deg 0.807 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.115 r_dihedral_angle_4_deg 18.745 r_dihedral_angle_3_deg 14.979 r_dihedral_angle_1_deg 6.248 r_mcangle_it 2.576 r_mcbond_it 1.718 r_mcbond_other 1.717 r_angle_refined_deg 1.414 r_angle_other_deg 0.807 r_chiral_restr 0.084 r_bond_refined_d 0.01 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 17604 Nucleic Acid Atoms Solvent Atoms 1149 Heterogen Atoms 48
Software Software Software Name Purpose SCALEPACK data reduction REFMAC refinement PDB_EXTRACT data extraction SCALEPACK data scaling