7AX7

Crystal structure of the Xyl-CE4 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C71 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5292.210 mg/mL in 20 mM Tris-HCl pH 7.5, 10 mM NaCl, 8 % (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1743.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.13α = 90
b = 59.7β = 90
c = 86.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442017-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.9323.07990.0190.9992.7421351213.713555817
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1296.90.991

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2C712.0500018162719.54137754561.43761508031351268399.88172678890.1762919329680.1728655639290.2427793906814.1404325504
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.4408772302
f_angle_d0.707693815628
f_chiral_restr0.0485426672537
f_bond_d0.00635143631305
f_plane_restr0.00427123583596
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1610
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms5

Software

Software
Software NamePurpose
HKL-3000data collection
d*TREKdata reduction
d*TREKdata scaling
d*TREKdata processing
d*TREKdata scaling
PHASERphasing
PHASERrefinement