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N-acetylglucosamine 6-phosphate dehydratase: inhibited 6-phosphogluconic acid state of NagS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel 3cvj
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 2.0 M Ammonium sulphate, 0.1 M BIS-Tris, pH 5.5; after crystallosation, crystals were soaked in mother liquor with 10-20% glycerol as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.668 α = 90 b = 87.668 β = 90 c = 278.81 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER X 9M 2019-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9 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 1.69 46.5 100 1 20.9 19.7 75437 35.45
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 1.69 1.72 0.799 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.69 46.47 1.35 71889 3548 99.9 0.1815 0.1803 0.1806 0.2051 0.2054 44.88
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.7519 f_angle_d 1.2281 f_chiral_restr 0.0817 f_bond_d 0.0148 f_plane_restr 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3626 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing