6G00 | pdb_00006g00

Crystal Structure of a GH8 xylanase from Teredinibacter turnerae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WU4 

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1WU41.456.9776616392499.170.153690.152790.160.171420.18RANDOM14.305
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
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