5FLW

Crystal structure of putative exo-beta-1,3-galactanase from Bifidobacterium bifidum s17


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NQHPDB ENTRY 3NQH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.05 M CALCIUM CHLORIDE DEHYDRATE, 0.1 M BIS-TRIS PH 6.5 AND 30% (V/V) POLYETHYLENE GLYCOL MONOMETHYL 550
Crystal Properties
Matthews coefficientSolvent content
3.2462

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.926α = 90
b = 67.343β = 90
c = 202.126γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4CNSLSX4C

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
11.447.699.90.0616.681745502
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)
11.41.4299.81.021.97.8

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 3NQH1.40119.9391.34174374177399.960.16180.16190.1834
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_d16.022
f_angle_d1.088
f_chiral_restr0.1
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4788
Nucleic Acid Atoms
Solvent Atoms1261
Heterogen Atoms14

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing