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The N253R mutant structures of trehalose synthase from Deinococcus radiodurans display two different active-site conformations
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 7 288 8% PEG 4000, 0.2M sodium acetate trihydrate, 0.3
M Tris-HCl (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.383 α = 90 b = 134.058 β = 90 c = 197.198 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 RAYONIX MX300HE 2014-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.91 20 96.2 11.8 3.6 54418
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 2.91 3.01 92.9 0.51 2.1 3.3
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 2.93 20 51664 2696 95.2 0.18592 0.18169 0.26676 0.2298 RANDOM 54.392
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] 4.53 0.32 -4.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_3_deg 17.999 r_dihedral_angle_4_deg 17.454 r_long_range_B_refined 8.516 r_long_range_B_other 8.514 r_dihedral_angle_1_deg 6.985 r_scangle_other 5.782 r_mcangle_it 5.611 r_mcangle_other 5.611 r_scbond_it 3.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_3_deg 17.999 r_dihedral_angle_4_deg 17.454 r_long_range_B_refined 8.516 r_long_range_B_other 8.514 r_dihedral_angle_1_deg 6.985 r_scangle_other 5.782 r_mcangle_it 5.611 r_mcangle_other 5.611 r_scbond_it 3.619 r_scbond_other 3.619 r_mcbond_it 3.559 r_mcbond_other 3.553 r_angle_refined_deg 1.562 r_angle_other_deg 0.85 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 17628 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing