5JOY | pdb_00005joy

Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraLOG


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
2.346.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.591α = 90
b = 91.505β = 90
c = 154.155γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9795DiamondI03

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
11.946.4999.80.170.9948.67.984685
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)
11.91.9399.61.441.67.7

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 deposited1.946.4980337427199.580.180730.178770.190.217960.22RANDOM23.966
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]
-0.160.33-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.768
r_dihedral_angle_4_deg16.147
r_dihedral_angle_3_deg11.735
r_dihedral_angle_1_deg6.89
r_long_range_B_refined4.937
r_long_range_B_other4.937
r_scangle_other2.106
r_mcangle_it1.892
r_mcangle_other1.892
r_angle_refined_deg1.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.768
r_dihedral_angle_4_deg16.147
r_dihedral_angle_3_deg11.735
r_dihedral_angle_1_deg6.89
r_long_range_B_refined4.937
r_long_range_B_other4.937
r_scangle_other2.106
r_mcangle_it1.892
r_mcangle_other1.892
r_angle_refined_deg1.382
r_scbond_it1.295
r_scbond_other1.295
r_mcbond_it1.168
r_mcbond_other1.168
r_angle_other_deg0.922
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms7837
Nucleic Acid Atoms
Solvent Atoms996
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing