5A6L

High resolution structure of the thermostable glucuronoxylan endo-Beta-1, 4-xylanase, CtXyn30A, from Clostridium thermocellum with two xylobiose units bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UQEPDBE ENTRY 4UQE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M POTASSIUM PHOSPHATE
Crystal Properties
Matthews coefficientSolvent content
2.5752.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.133α = 90
b = 87.249β = 114.68
c = 60.027γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-17MSINGLE 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
11.846.251000.2817.53.8435179.8
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)
11.81.841001.499.83.8

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 REPLACEMENTTHROUGHOUTPDBE ENTRY 4UQE1.854.5441363212899.970.137120.13580.16242RANDOM9.888
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]
0.01-0.160.18-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.338
r_dihedral_angle_4_deg20.189
r_dihedral_angle_3_deg11.678
r_dihedral_angle_1_deg6.613
r_angle_refined_deg1.763
r_angle_other_deg1.023
r_scbond_it0.91
r_mcangle_it0.731
r_mcbond_it0.419
r_mcbond_other0.417
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.338
r_dihedral_angle_4_deg20.189
r_dihedral_angle_3_deg11.678
r_dihedral_angle_1_deg6.613
r_angle_refined_deg1.763
r_angle_other_deg1.023
r_scbond_it0.91
r_mcangle_it0.731
r_mcbond_it0.419
r_mcbond_other0.417
r_chiral_restr0.109
r_bond_refined_d0.018
r_gen_planes_refined0.01
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3114
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing