5OYE

GH5 endo-xyloglucanase from Cellvibrio japonicus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.5291ammonium sulphate, MES buffer
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.343α = 90
b = 95.83β = 90
c = 157.208γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.981.831000.0810.0310.9988.57.766811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.941000.5920.8137.6

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 REPLACEMENTTHROUGHOUT5OYC.PDB1.981.8363393329999.910.23740.234150.29997RANDOM53.356
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]
-0.67.41-6.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.291
r_dihedral_angle_4_deg18.737
r_dihedral_angle_3_deg14.962
r_long_range_B_other7.997
r_long_range_B_refined7.995
r_dihedral_angle_1_deg7.683
r_scangle_other6.612
r_mcangle_it6.601
r_mcangle_other6.6
r_mcbond_it5.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.291
r_dihedral_angle_4_deg18.737
r_dihedral_angle_3_deg14.962
r_long_range_B_other7.997
r_long_range_B_refined7.995
r_dihedral_angle_1_deg7.683
r_scangle_other6.612
r_mcangle_it6.601
r_mcangle_other6.6
r_mcbond_it5.096
r_mcbond_other5.094
r_scbond_it5.073
r_scbond_other5.073
r_angle_refined_deg1.933
r_angle_other_deg1.143
r_chiral_restr0.133
r_bond_refined_d0.018
r_gen_planes_refined0.009
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 Atoms5825
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms168

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing