5FKQ

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
otherAPO STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M SODIUM ACETATE (PH 5.0), 0.6 M SODIUM FORMATE, 8 % W/V PGA-LM
Crystal Properties
Matthews coefficientSolvent content
2.6152.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.002α = 90
b = 94.116β = 103.27
c = 105.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PIXEL2015-02-14MSINGLE 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
11.7148.8899.80.1114.11723922
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)
11.711.7599.70.731.64.2

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 REPLACEMENTTHROUGHOUTAPO STRUCTURE1.71102.82163901855699.90.194080.192480.22462RANDOM14.691
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]
-0.611.58-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.193
r_dihedral_angle_4_deg16.682
r_dihedral_angle_3_deg11.862
r_dihedral_angle_1_deg7.356
r_angle_refined_deg1.827
r_mcangle_it1.634
r_scbond_it1.482
r_mcbond_it1.132
r_mcbond_other1.132
r_angle_other_deg1.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.193
r_dihedral_angle_4_deg16.682
r_dihedral_angle_3_deg11.862
r_dihedral_angle_1_deg7.356
r_angle_refined_deg1.827
r_mcangle_it1.634
r_scbond_it1.482
r_mcbond_it1.132
r_mcbond_other1.132
r_angle_other_deg1.057
r_chiral_restr0.115
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11083
Nucleic Acid Atoms
Solvent Atoms961
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing