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Crystal structure of Tannerella forsythia sugar kinase K1058 in complex with N-acetylmuramic acid (MurNAc)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 1.5 M ammonium sulfate, 0.1 M Tris pH 8.5, 12% (v/v) glycerol 2 VAPOR DIFFUSION, SITTING DROP 8.5 277 1.5 M ammonium sulfate, 0.1 M Tris pH 8.5, 12% (v/v) glycerol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.75 α = 90 b = 143.75 β = 90 c = 210.95 γ = 120
Symmetry Space Group P 31 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-F 2022-02-05 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2022-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA 2 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.06 48.585 100 0.99 7.97 20.38 48712 74.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.06 3.23 0.363
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.06 29.85 48103 1444 99.855 0.22 0.2192 0.2454 0.2115 86.954
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] 0.006 0.003 0.006 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.074 r_dihedral_angle_6_deg 8.848 r_dihedral_angle_2_deg 5.955 r_lrange_it 5.521 r_dihedral_angle_1_deg 4.601 r_scangle_it 2.076 r_mcangle_it 2.06 r_scbond_it 1.267 r_mcbond_it 1.197 r_angle_refined_deg 0.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.074 r_dihedral_angle_6_deg 8.848 r_dihedral_angle_2_deg 5.955 r_lrange_it 5.521 r_dihedral_angle_1_deg 4.601 r_scangle_it 2.076 r_mcangle_it 2.06 r_scbond_it 1.267 r_mcbond_it 1.197 r_angle_refined_deg 0.609 r_nbtor_refined 0.305 r_nbd_refined 0.161 r_symmetry_nbd_refined 0.138 r_xyhbond_nbd_refined 0.077 r_symmetry_xyhbond_nbd_refined 0.055 r_chiral_restr 0.046 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13091 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 185
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing