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Crystal structure of Tannerella forsythia MurNAc kinase MurK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2-0.3 M ammonium sulfate, 14-22% (w/v) PEG3350, bis-tris/citric acid pH 4.1-6.4
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.759 α = 74.3 b = 59.51 β = 75.274 c = 96.708 γ = 65.953
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 EIGER2 XE 16M 2018-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 2.05 49.503 96.1 0.997 9.06 2.37 68635
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 2.05 2.17 0.751
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1X7F 2.05 49.503 68630 1716 96.216 0.202 0.2006 0.2486 0.2315 37.311
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] -0.936 0.221 -1.089 2.483 1.892 -1.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.358 r_dihedral_angle_6_deg 13.693 r_dihedral_angle_2_deg 11.515 r_dihedral_angle_1_deg 6.613 r_lrange_it 6.131 r_scangle_it 2.542 r_scbond_it 1.764 r_mcangle_it 1.619 r_angle_refined_deg 1.126 r_mcbond_it 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.358 r_dihedral_angle_6_deg 13.693 r_dihedral_angle_2_deg 11.515 r_dihedral_angle_1_deg 6.613 r_lrange_it 6.131 r_scangle_it 2.542 r_scbond_it 1.764 r_mcangle_it 1.619 r_angle_refined_deg 1.126 r_mcbond_it 1.027 r_nbtor_refined 0.307 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.213 r_xyhbond_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.146 r_chiral_restr 0.092 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8679 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing