☰ Navigation Tabs
Structure of N-acetylglucosamine kinase from Plesiomonas shigelloides in complex with AMP-PNP in the absence of N-acetylglucoseamine substrate
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 0.09M NPS; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K, condition C9 from Morpheus crystallisation screen (Molecular Dimensions).
Crystal Properties Matthews coefficient Solvent content 2.96 58.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.265 α = 90 b = 121.265 β = 90 c = 91.684 γ = 120
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 2019-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 2.2 60.63 99.2 0.964 5.2 3.3 38637
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 2.27 0.396
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 4DB3 2.2 39.693 38630 1846 99.168 0.21 0.2076 0.2517 0.2169 47.045
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] 0.417 0.209 0.417 -1.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.653 r_dihedral_angle_4_deg 17.484 r_dihedral_angle_3_deg 17.306 r_lrange_it 13.405 r_scangle_it 12.619 r_scbond_it 10.454 r_mcangle_it 7.469 r_mcbond_it 6.459 r_dihedral_angle_1_deg 5.782 r_angle_refined_deg 1.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.653 r_dihedral_angle_4_deg 17.484 r_dihedral_angle_3_deg 17.306 r_lrange_it 13.405 r_scangle_it 12.619 r_scbond_it 10.454 r_mcangle_it 7.469 r_mcbond_it 6.459 r_dihedral_angle_1_deg 5.782 r_angle_refined_deg 1.563 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.205 r_chiral_restr 0.119 r_symmetry_xyhbond_nbd_refined 0.118 r_xyhbond_nbd_refined 0.113 r_ncsr_local_group_1 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4630 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing DM phasing MOLREP phasing