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Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase from Mycobacterium smegmatis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295.15 NagA crystals grew in a condition containing 0.12 M monosaccharide mix (Morpheus, Molecular Dimensions), 0.1 M imidazole/MES pH 6.5, 20 % PEG 500 MME, 10 % w/v PEG 20000 with the addition of 10 mM CdCl2 additive.
Crystal Properties Matthews coefficient Solvent content 2.66 53.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.45 α = 88.12 b = 86.39 β = 75.58 c = 89.93 γ = 69.79
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-F 2017-05-22 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.58 55.23 98.2 0.173 0.245 0.173 0.96 4.3 2.6 51044
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.6296 98 0.902 0.059 0.902 0.434 1 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2P50 2.58 51.951 1.96 51006 2494 98.15 0.2496 0.2473 0.2482 0.2951 0.2959
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 4.563 f_angle_d 0.957 f_chiral_restr 0.057 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10714 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building O model building