6X8D

Arabinose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5J6Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH72980.2 M calcium chloride, 0.1 M HEPES (pH 7), 20% (v/v) polyethylene glycol 3350 and 30 % (w/v) arabinose
Crystal Properties
Matthews coefficientSolvent content
2.2445.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.12α = 90
b = 50.71β = 90
c = 79.62γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS3 S 6M2020-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
10.9642.7795.170.06719.1111064257.31
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.960.990.685

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5j6y142.771.34982394912990.14710.14610.165913.96
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_d14.6042
f_angle_d1.6722
f_chiral_restr0.1203
f_bond_d0.0171
f_plane_restr0.0133
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1361
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms28

Software

Software
Software NamePurpose
PHENIXrefinement