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Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AF6 PDB ENTRY 2AF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 52.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.806 α = 90 b = 95.806 β = 90 c = 64.637 γ = 90
Symmetry Space Group P 42 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.3 30 0.045 9.1 13929
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) 2.3 2.38 0.492 3.61 6.2
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 PDB ENTRY 2AF6 2.3 27.43 13196 670 99.87 0.22453 0.22272 0.2247 0.25952 0.2279 RANDOM 47.685
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] -0.07 -0.07 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.027 r_dihedral_angle_4_deg 20.074 r_dihedral_angle_3_deg 15.927 r_dihedral_angle_1_deg 6.524 r_scangle_it 3.4 r_scbond_it 2.088 r_mcangle_it 1.693 r_angle_refined_deg 1.347 r_mcbond_it 0.985 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.027 r_dihedral_angle_4_deg 20.074 r_dihedral_angle_3_deg 15.927 r_dihedral_angle_1_deg 6.524 r_scangle_it 3.4 r_scbond_it 2.088 r_mcangle_it 1.693 r_angle_refined_deg 1.347 r_mcbond_it 0.985 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1790 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 53
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling