☰ Navigation Tabs
N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate
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 90 mM halogens; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K,
condition B9 from Morpheus screen (Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 3.42 64.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.508 α = 90 b = 114.508 β = 90 c = 119.266 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 2016-11-28 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 1.75 99.17 99.1 0.998 8.4 3.8 90389
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 1.75 1.78 0.194
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 1.75 76.252 90350 4568 99.02 0.194 0.1929 0.193 0.2226 0.2225 36.515
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] -0.012 -0.006 -0.012 0.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.837 r_dihedral_angle_4_deg 15.786 r_dihedral_angle_3_deg 15.214 r_lrange_it 11.616 r_scangle_it 10.111 r_scbond_it 8.059 r_mcangle_it 7.299 r_mcbond_it 6.253 r_dihedral_angle_1_deg 5.724 r_angle_refined_deg 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.837 r_dihedral_angle_4_deg 15.786 r_dihedral_angle_3_deg 15.214 r_lrange_it 11.616 r_scangle_it 10.111 r_scbond_it 8.059 r_mcangle_it 7.299 r_mcbond_it 6.253 r_dihedral_angle_1_deg 5.724 r_angle_refined_deg 1.75 r_metal_ion_refined 0.345 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.23 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.112 r_symmetry_xyhbond_nbd_refined 0.111 r_ncsr_local_group_1 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4646 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing DM phasing MOLREP phasing