5FKR

Unraveling the first step of xyloglucan degradation by the soil saprophyte Cellvibrio japonicus through the functional and structural characterization of a potent GH74 endo-xyloglucanase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LGN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M TRIS (PH 7.8), 0.3 M POTASSIUM BROMIDE, 8 % PGA-LM
Crystal Properties
Matthews coefficientSolvent content
2.7254.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.89α = 90
b = 131.91β = 90
c = 73.17γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M-F2014-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.2873.1799.80.1311.46.5395062
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)
12.282.3499.60.622.86.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4LGN2.2873.1737512194899.770.212650.209690.26836RANDOM28.639
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]
-1.896.14-4.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.785
r_dihedral_angle_4_deg16.65
r_dihedral_angle_3_deg13.813
r_dihedral_angle_1_deg7.594
r_long_range_B_refined4.294
r_long_range_B_other4.265
r_mcangle_it2.805
r_mcangle_other2.805
r_scangle_other2.75
r_mcbond_it1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.785
r_dihedral_angle_4_deg16.65
r_dihedral_angle_3_deg13.813
r_dihedral_angle_1_deg7.594
r_long_range_B_refined4.294
r_long_range_B_other4.265
r_mcangle_it2.805
r_mcangle_other2.805
r_scangle_other2.75
r_mcbond_it1.84
r_mcbond_other1.84
r_scbond_it1.804
r_scbond_other1.804
r_angle_refined_deg1.658
r_angle_other_deg1.023
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5538
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing