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N-acetylglucosamine 6-phosphate dehydratase: GlcNAc6P substrate-bound state of NagS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 3.06 59.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.366 α = 90 b = 88.366 β = 90 c = 284.455 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 PILATUS3 6M 2016-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9760 ESRF ID29
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 2.59 45.7 99.9 0.998 9.7 18.9 21362 54.66
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 2.59 2.68 0.527
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 2.59 45.66 1.35 21362 1098 99.93 0.1924 0.1904 0.1906 0.2292 0.2294 60.61
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 12.7899 f_angle_d 0.628 f_chiral_restr 0.0441 f_plane_restr 0.0082 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3626 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling CRANK2 phasing