6Q2F

Structure of Rhamnosidase from Novosphingobium sp. PP1Y


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1 M MES, pH 6.8, 6-7% Tascimate pH 5.0, 2-10 mM Tris, pH 7.5, 10 % w/w PEG 20K, 6-10% glycerol, and 0.01% NaN3
Crystal Properties
Matthews coefficientSolvent content
3.1661.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.809α = 90
b = 114.57β = 90
c = 158.797γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2018-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.979SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.2000007494439.799.90.09214.26.714426230.4712029358
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.200000749442.250.4623.7

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-FreeMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE2.2000007494439.699251.89205264243144262697599.79868975390.1635410153280.1628517873760.17704612150943.4570003117
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.3245778265
f_angle_d1.02650879138
f_chiral_restr0.0687153025182
f_bond_d0.00994388297688
f_plane_restr0.00599732907706
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8079
Nucleic Acid Atoms
Solvent Atoms732
Heterogen Atoms1

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing