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Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides
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 Tris/bicine pH 8.5; 12.5% each MPD, PEG 1K, PEG 3350.
condition A12 from Morpheus screen (Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.57 52.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.23 α = 90 b = 95.23 β = 90 c = 180.55 γ = 120
Symmetry Space Group P 31 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 PILATUS3 6M 2017-09-27 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 1.7 75.01 99.6 0.999 13.8 5 104319
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 1.7 1.73 99.7 0.27 5.1
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 1.7 60.888 104239 5218 99.517 0.184 0.1827 0.1827 0.2103 0.2105 43.654
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] 1.128 0.564 1.128 -3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.223 r_dihedral_angle_4_deg 17.493 r_dihedral_angle_3_deg 15.679 r_lrange_it 9.044 r_scangle_it 8.742 r_scbond_it 7.307 r_dihedral_angle_1_deg 5.663 r_mcangle_it 5.284 r_mcbond_it 4.784 r_angle_refined_deg 1.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.223 r_dihedral_angle_4_deg 17.493 r_dihedral_angle_3_deg 15.679 r_lrange_it 9.044 r_scangle_it 8.742 r_scbond_it 7.307 r_dihedral_angle_1_deg 5.663 r_mcangle_it 5.284 r_mcbond_it 4.784 r_angle_refined_deg 1.617 r_nbtor_refined 0.314 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.138 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.114 r_ncsr_local_group_1 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4639 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing DM model building BUSTER refinement