6X7T

Allose-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
1MICROBATCH7298~0.2 M calcium chloride, ~0.1 M HEPES (pH 7), ~20% (v/v) polyethylene glycol 3350 and ~30 % (w/v) Allose
Crystal Properties
Matthews coefficientSolvent content
2.1943.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.47α = 90
b = 50.27β = 90
c = 79.01γ = 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)R Merge 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
10.9642.4195.550.05823.111.21061227.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.960.990.638

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-VALUE5j6y142.411.3497423487199.020.12720.12710.130211.42
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_d11.6847
f_angle_d1.5584
f_chiral_restr0.2208
f_bond_d0.0113
f_plane_restr0.0078
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1376
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms30

Software

Software
Software NamePurpose
PHENIXrefinement