5JOW | pdb_00005jow

Bacteroides ovatus Xyloglucan PUL GH43A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherGH43B to be deposited

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22920.1 M Tris pH 7.2 - 7.8, 0.18 M magnesium chloride and 12% (w/v) PEG-6000
Crystal Properties
Matthews coefficientSolvent content
2.3247.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.432α = 90
b = 91.172β = 90
c = 156.856γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.920DiamondI04-1

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
11.646.691000.0920.99914.58.1142867
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)
11.61.631001.051.98

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTGH43B to be deposited1.646.69135666711599.910.127350.125280.140.166980.17RANDOM20.095
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]
-0.20.5-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.18
r_dihedral_angle_4_deg15.259
r_dihedral_angle_3_deg10.906
r_sphericity_bonded8.788
r_dihedral_angle_1_deg6.77
r_long_range_B_refined4.315
r_long_range_B_other4.315
r_scangle_other2.37
r_mcangle_it2.037
r_mcangle_other2.037
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.18
r_dihedral_angle_4_deg15.259
r_dihedral_angle_3_deg10.906
r_sphericity_bonded8.788
r_dihedral_angle_1_deg6.77
r_long_range_B_refined4.315
r_long_range_B_other4.315
r_scangle_other2.37
r_mcangle_it2.037
r_mcangle_other2.037
r_scbond_it1.971
r_scbond_other1.971
r_rigid_bond_restr1.538
r_mcbond_it1.53
r_mcbond_other1.53
r_angle_refined_deg1.365
r_angle_other_deg0.927
r_chiral_restr0.091
r_bond_refined_d0.009
r_gen_planes_refined0.006
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_scangle_it
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7898
Nucleic Acid Atoms
Solvent Atoms1315
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing