5JOU

Bacteroides ovatus Xyloglucan PUL GH31


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XVG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2920.2 M potassium thiocyanate, 14-20% (w/v) PEG-3350
Crystal Properties
Matthews coefficientSolvent content
2.7755.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.892α = 90
b = 109.02β = 90
c = 145.064γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-12-12MSINGLE 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
11.548.3596.70.1240.99712.47.5187821
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)
11.51.5374.51.0914.2

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 REPLACEMENTTHROUGHOUT2xvg1.548.35178283944496.530.161230.160040.18354RANDOM14.903
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]
-0.52-0.410.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.775
r_dihedral_angle_4_deg15.521
r_dihedral_angle_3_deg11.149
r_long_range_B_refined6.788
r_long_range_B_other6.788
r_dihedral_angle_1_deg6.594
r_scangle_other1.988
r_angle_refined_deg1.41
r_mcangle_it1.246
r_mcangle_other1.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.775
r_dihedral_angle_4_deg15.521
r_dihedral_angle_3_deg11.149
r_long_range_B_refined6.788
r_long_range_B_other6.788
r_dihedral_angle_1_deg6.594
r_scangle_other1.988
r_angle_refined_deg1.41
r_mcangle_it1.246
r_mcangle_other1.246
r_scbond_it1.241
r_scbond_other1.241
r_angle_other_deg0.924
r_mcbond_it0.768
r_mcbond_other0.763
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms7631
Nucleic Acid Atoms
Solvent Atoms1644
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing