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Crystal structure of Tannerella forsythia sugar kinase K1058
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X7F 1X7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Sodium cacodylate, MPD, PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.94 α = 90 b = 131.94 β = 90 c = 89.22 γ = 90
Symmetry Space Group I 41 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 100 PIXEL DECTRIS PILATUS 2M-F 2018-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 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 2 49.216 100 0.999 19.58 26.63 26844
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 2.05 0.534
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1X7F 2 49.216 26843 1343 99.985 0.179 0.1771 0.1771 0.2057 0.206 41.513
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] -0.277 -0.277 0.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.699 r_dihedral_angle_6_deg 15.457 r_dihedral_angle_3_deg 14.512 r_lrange_it 8.264 r_scangle_it 6.887 r_dihedral_angle_1_deg 6.335 r_scbond_it 5.735 r_mcangle_it 4.031 r_mcbond_it 3.594 r_angle_refined_deg 1.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.699 r_dihedral_angle_6_deg 15.457 r_dihedral_angle_3_deg 14.512 r_lrange_it 8.264 r_scangle_it 6.887 r_dihedral_angle_1_deg 6.335 r_scbond_it 5.735 r_mcangle_it 4.031 r_mcbond_it 3.594 r_angle_refined_deg 1.464 r_nbtor_refined 0.315 r_nbd_refined 0.207 r_symmetry_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.137 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.09 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2183 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing