5OYD

GH5 endo-xyloglucanase from Cellvibrio japonicus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5291ammonium sulphate, MES buffer
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.455α = 90
b = 97.598β = 90
c = 157.196γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97948DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.183.051000.0620.99812.86.250763
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.161000.5470.9336.3

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.PDB2.183.0548113252599.830.221060.217790.28293RANDOM48.033
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]
-0.223.89-3.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.13
r_dihedral_angle_4_deg19.704
r_dihedral_angle_3_deg14.994
r_dihedral_angle_1_deg6.988
r_long_range_B_refined6.833
r_long_range_B_other6.833
r_scangle_other5.556
r_mcangle_other5.338
r_mcangle_it5.336
r_scbond_it4.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.13
r_dihedral_angle_4_deg19.704
r_dihedral_angle_3_deg14.994
r_dihedral_angle_1_deg6.988
r_long_range_B_refined6.833
r_long_range_B_other6.833
r_scangle_other5.556
r_mcangle_other5.338
r_mcangle_it5.336
r_scbond_it4.262
r_scbond_other4.259
r_mcbond_other4.161
r_mcbond_it4.16
r_angle_refined_deg1.793
r_angle_other_deg1.086
r_chiral_restr0.104
r_bond_refined_d0.017
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 Atoms5792
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms178

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing