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N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine
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 Na-HEPES/MOPS pH 7.5; 12.5% each MPD, PEG 1K, PEG 3350
Condition B8 of Morpheus screen (Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.476 α = 90 b = 115.476 β = 90 c = 119.657 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 2018-08-05 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 1.94 57.74 100 0.999 11 6.7 68568
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 1.94 1.99 0.282
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 1.94 46.136 68526 3517 99.975 0.211 0.209 0.2091 0.2497 0.2498 55.854
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] 0.288 0.144 0.288 -0.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.908 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_3_deg 16.205 r_lrange_it 15.956 r_scangle_it 14.513 r_scbond_it 12.064 r_mcangle_it 11.197 r_mcbond_it 9.215 r_dihedral_angle_1_deg 6.278 r_angle_refined_deg 1.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.908 r_dihedral_angle_4_deg 16.51 r_dihedral_angle_3_deg 16.205 r_lrange_it 15.956 r_scangle_it 14.513 r_scbond_it 12.064 r_mcangle_it 11.197 r_mcbond_it 9.215 r_dihedral_angle_1_deg 6.278 r_angle_refined_deg 1.654 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.244 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.126 r_symmetry_xyhbond_nbd_refined 0.114 r_chiral_restr 0.11 r_ncsr_local_group_1 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4630 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing DM phasing MOLREP phasing BUSTER refinement