4UQB | pdb_00004uqb

X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum at 1.68 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CKQPDB ENTRY 4CKQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES 7.5, 10 % (V/V)PEG 8000, 8 % (V/V)ETHILE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
2.5251.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.98α = 114.77
b = 50.59β = 101.43
c = 59.31γ = 103.85
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rKIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL2014-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.6850.6892.30.0813.634.3476511.77
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)
11.681.7477.20.831.774

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4CKQ1.6845.4945706194592.310.1810.1790.190.2060.21RANDOM27.8
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]
-2.34-1.32-0.490.722.13-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.015
r_dihedral_angle_3_deg12.463
r_dihedral_angle_4_deg12.463
r_dihedral_angle_1_deg6.316
r_angle_refined_deg1.212
r_mcbond_it0.79
r_mcbond_other0.789
r_angle_other_deg0.746
r_chiral_restr0.071
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3128
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing