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N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and AMP-PNP inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 60 mM divalent cations; 0.1 M imidazole/MES pH 6.5; 30% each glycerol and PEG 4K. Condition A3 from Morpheus screen (Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.202 α = 90 b = 115.202 β = 90 c = 120.36 γ = 120
Symmetry Space Group P 32 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 6M 2018-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.11 57.6 100 0.998 9.5 10 53533
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 2.11 2.17 0.336
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 4DB3 2.11 29.107 53472 2794 99.935 0.194 0.1914 0.1919 0.233 0.2331 50.004
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] -1.845 -0.923 -1.845 5.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.611 r_dihedral_angle_4_deg 18.71 r_dihedral_angle_3_deg 16.602 r_lrange_it 12.784 r_scangle_it 11.505 r_scbond_it 9.263 r_mcangle_it 8.212 r_mcbond_it 6.802 r_dihedral_angle_1_deg 5.817 r_angle_refined_deg 1.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.611 r_dihedral_angle_4_deg 18.71 r_dihedral_angle_3_deg 16.602 r_lrange_it 12.784 r_scangle_it 11.505 r_scbond_it 9.263 r_mcangle_it 8.212 r_mcbond_it 6.802 r_dihedral_angle_1_deg 5.817 r_angle_refined_deg 1.565 r_nbtor_refined 0.314 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.118 r_metal_ion_refined 0.113 r_chiral_restr 0.106 r_ncsr_local_group_1 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4650 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing DM phasing MOLREP phasing