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Crystal structure of trehalose synthase from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZOA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 15 % PEG 4000, 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl (pH 8.5)
Crystal Properties Matthews coefficient Solvent content 2.46 49.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.609 α = 90 b = 195.896 β = 92.89 c = 130.986 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX300HE 2013-03-24 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) 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 2.7 30 97.7 0.096 9.2 3.6 128557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 89.4 0.408 3.3 11771
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ZOA 2.7 30 122065 6455 97.62 0.19586 0.19372 0.1971 0.23626 0.2387 RANDOM 37.461
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] 3.01 2.54 -1.9 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.228 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 17.439 r_long_range_B_refined 6.55 r_long_range_B_other 6.538 r_dihedral_angle_1_deg 5.9 r_scangle_other 4.167 r_mcangle_it 4.005 r_mcangle_other 4.005 r_scbond_it 2.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.228 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 17.439 r_long_range_B_refined 6.55 r_long_range_B_other 6.538 r_dihedral_angle_1_deg 5.9 r_scangle_other 4.167 r_mcangle_it 4.005 r_mcangle_other 4.005 r_scbond_it 2.528 r_scbond_other 2.528 r_mcbond_it 2.491 r_mcbond_other 2.489 r_angle_refined_deg 1.416 r_angle_other_deg 1.313 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35232 Nucleic Acid Atoms Solvent Atoms 979 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement SCALEPACK data reduction PDB_EXTRACT data extraction SCALEPACK data scaling