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Crystal structure of engineered thermostable D-tagatose 3-epimerase PcDTE-Var8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 293 0.1M Tris, 18% w/v PEG 8000, 0.2M lithium sulfate, pH 7.7, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.47 α = 90 b = 47.5 β = 103.68 c = 124.73 γ = 90
Symmetry Space Group C 1 2 1
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 2M 2013-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
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 1.8 53.73 99.6 0.057 11.2 3.1 58427
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 1.8 1.84 99.6 0.378 3.1 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 (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 2qul 1.8 53.73 55465 2957 99.47 0.17809 0.17643 0.1863 0.20781 0.2107 RANDOM 31.902
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] 0.32 -0.44 0.85 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.588 r_dihedral_angle_4_deg 16.85 r_dihedral_angle_3_deg 13.391 r_dihedral_angle_1_deg 6.06 r_angle_refined_deg 1.484 r_angle_other_deg 0.946 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.588 r_dihedral_angle_4_deg 16.85 r_dihedral_angle_3_deg 13.391 r_dihedral_angle_1_deg 6.06 r_angle_refined_deg 1.484 r_angle_other_deg 0.946 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.006 r_bond_other_d 0.004 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4667 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 33
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction