6NWZ

Crystal structure of Agd3 a novel carbohydrate deacetylase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.7 % (w/v) PEG 400, 15 % (v/v) glycerol, 1.7 M ammonium sulfate, 0.25 % (w/v) PEG3350, 85 mM HEPES pH 7.5
2VAPOR DIFFUSION, HANGING DROP7.52931.7 % (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 coefficientSolvent content
3.8868.29
3.8868.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.97α = 90
b = 77.97β = 90
c = 640.31γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-07-11MSINGLE WAVELENGTH
22x-ray100PIXELDECTRIS EIGER X 16M2017-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-11.28308NSLS-II17-ID-1
2SYNCHROTRONNSLS-II BEAMLINE 17-ID-11.28308NSLS-II17-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.5929.8786.130.024670.034890.024670.99917.91237314
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)RedundancyNumber Unique Reflections (All)
12.592.69413.570.3640.3640.2570.968

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.629.8651.3632191169086.170.19230.18950.2423Random47.4631
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 AtomsNumber
Protein Atoms5095
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms90

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHASERphasing
PDB_EXTRACTdata extraction