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N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and ADP
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 291 120 mM alcohols; ; 0.1 M imidazole/MES pH 6.5; 30% each glycerol and PEG 4K
Condition A3 of Morpheus screen (Molecular dimensions). Crystal was soaked for 60 seconds in cryoprotectant containing 10 mM
ADP
Crystal Properties Matthews coefficient Solvent content 2.5 50.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.1 α = 90 b = 115.1 β = 90 c = 120.304 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 12M 2018-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.57 99.68 100 0.999 12.7 9.9 128365
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 1.57 1.6 100 0.291
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 1.57 99.68 128293 6471 99.981 0.187 0.1857 0.1857 0.2112 0.2111 29.979
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] -0.198 -0.099 -0.198 0.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.533 r_dihedral_angle_4_deg 15.494 r_dihedral_angle_3_deg 14.208 r_lrange_it 8.07 r_scangle_it 6.611 r_dihedral_angle_1_deg 5.845 r_scbond_it 5.01 r_mcangle_it 3.829 r_mcbond_it 3.173 r_angle_refined_deg 1.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.533 r_dihedral_angle_4_deg 15.494 r_dihedral_angle_3_deg 14.208 r_lrange_it 8.07 r_scangle_it 6.611 r_dihedral_angle_1_deg 5.845 r_scbond_it 5.01 r_mcangle_it 3.829 r_mcbond_it 3.173 r_angle_refined_deg 1.447 r_nbtor_refined 0.312 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.201 r_metal_ion_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.128 r_ncsr_local_group_1 0.099 r_chiral_restr 0.096 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4648 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 207
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing xia2 data scaling