5JP0

Bacteroides ovatus Xyloglucan PUL GH3B with bound glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EX1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2920.2 M sodium acetate, 15-25% PEG-3350
Crystal Properties
Matthews coefficientSolvent content
2.3547.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.169α = 90
b = 104.068β = 90
c = 160.444γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-12-16MSINGLE 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
12.347.5799.90.1510.99511.48.172918
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)
12.32.351000.9232.18.5

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 REPLACEMENTTHROUGHOUT1ex12.347.5769286356199.850.178630.176970.21086RANDOM35.059
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]
1.52-0.12-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.586
r_dihedral_angle_4_deg18.979
r_dihedral_angle_3_deg12.511
r_dihedral_angle_1_deg6.641
r_long_range_B_other6.307
r_long_range_B_refined6.3
r_scangle_other5.441
r_scbond_it4.15
r_scbond_other4.149
r_mcangle_it3.684
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.586
r_dihedral_angle_4_deg18.979
r_dihedral_angle_3_deg12.511
r_dihedral_angle_1_deg6.641
r_long_range_B_other6.307
r_long_range_B_refined6.3
r_scangle_other5.441
r_scbond_it4.15
r_scbond_other4.149
r_mcangle_it3.684
r_mcangle_other3.683
r_mcbond_it2.811
r_mcbond_other2.811
r_angle_refined_deg1.412
r_angle_other_deg1.036
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms11508
Nucleic Acid Atoms
Solvent Atoms462
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing