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Crystal structure of the H51N mutant of the 3,4-ketoisomerase QdtA from Thermoanaerobacterium thermosaccharolyticum in complex with TDP-4-keto-6-deoxyglucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O9E PDB entry 4O9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 28-33% pentaerythritol propoxylate, 100 mM HEPPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.14 60.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.396 α = 90 b = 95.396 β = 90 c = 94.643 γ = 90
Symmetry Space Group P 4 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker Platinum 135 Montel mirrors 2013-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 50 95.7 0.079 0.079 14.9 7.7 33577 33577
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 87.1 0.374 0.374 1.9 2.1 4259
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 4O9E 1.9 29.97 33577 31868 1701 95.75 0.203 0.20258 0.20053 0.2072 0.24078 0.2434 RANDOM 28.137
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] 0.42 0.42 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.832 r_dihedral_angle_4_deg 19.355 r_dihedral_angle_3_deg 16.371 r_dihedral_angle_1_deg 8.1 r_angle_refined_deg 1.347 r_angle_other_deg 0.598 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.832 r_dihedral_angle_4_deg 19.355 r_dihedral_angle_3_deg 16.371 r_dihedral_angle_1_deg 8.1 r_angle_refined_deg 1.347 r_angle_other_deg 0.598 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_gen_planes_other 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 2300 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 99
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement SAINT data reduction SADABS data scaling