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Crystal structure of Agd3 a novel carbohydrate deacetylase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.7 % (w/v) PEG 400, 15 % (v/v) glycerol, 1.7 M ammonium sulfate, 0.25 % (w/v) PEG3350, 85 mM HEPES pH 7.5 2 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.7 % (w/v) PEG 400, 15 % (v/v) glycerol, 1.7 M ammonium sulfate, 0.25 % (w/v) PEG3350, 85 mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.88 68.29 3.88 68.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.97 α = 90 b = 77.97 β = 90 c = 640.31 γ = 120
Symmetry Space Group P 61 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 16M 2017-07-11 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 1.28308 NSLS-II 17-ID-1 2 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 1.28308 NSLS-II 17-ID-1
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 2.59 29.87 86.13 0.02467 0.03489 0.02467 0.999 17.91 2 37314
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 2.59 2.694 13.57 0.364 0.364 0.257 0.968
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.6 29.865 1.36 32191 1690 86.17 0.1923 0.1895 0.1887 0.2423 0.2403 Random 47.4631
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5095 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling SHELX phasing PHASER phasing PDB_EXTRACT data extraction