6G00

Crystal Structure of a GH8 xylanase from Teredinibacter turnerae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5291.2sodium acetate (0.1M, pH 5.0), NaCl (0.2 M), polyethylene glycol 6000 16%.
Crystal Properties
Matthews coefficientSolvent content
2.2645.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.54α = 90
b = 72.995β = 90
c = 90.866γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.98DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.45199.49.64.380610
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.42

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 REPLACEMENTTHROUGHOUT1WU41.456.9776616392499.170.153690.152790.17142RANDOM14.305
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]
0.940.54-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.938
r_dihedral_angle_4_deg17.741
r_dihedral_angle_3_deg11.894
r_dihedral_angle_1_deg5.632
r_long_range_B_refined3.837
r_long_range_B_other3.837
r_scangle_other2.917
r_scbond_it1.919
r_scbond_other1.919
r_angle_refined_deg1.683
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.938
r_dihedral_angle_4_deg17.741
r_dihedral_angle_3_deg11.894
r_dihedral_angle_1_deg5.632
r_long_range_B_refined3.837
r_long_range_B_other3.837
r_scangle_other2.917
r_scbond_it1.919
r_scbond_other1.919
r_angle_refined_deg1.683
r_mcangle_other1.569
r_mcangle_it1.567
r_mcbond_it1.06
r_mcbond_other1.053
r_angle_other_deg1.051
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.011
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 Atoms3139
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing