1UR2

Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with arabinofuranose alpha 1,3 linked to xylotriose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UQYPDB ENTRY 1UQY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.2M MGCL2 0.1M TRIS HCL PH8.5, 30% PEG 4K, 5% PEG 400., pH 8.50
Crystal Properties
Matthews coefficientSolvent content
236.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.924α = 90
b = 67.659β = 90
c = 104.782γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCDVERTICAL FOCUSING MIRROR2003-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
11.63098.30.0761.933.2542050
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)
11.61.6690.30.4321.932.23

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1UQY1.619.2842034220998.80.1540.1520.189RANDOM11.84
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]
0.29-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.813
r_dihedral_angle_4_deg16.235
r_dihedral_angle_3_deg13.845
r_dihedral_angle_1_deg6.128
r_scangle_it2.67
r_scbond_it1.849
r_angle_refined_deg1.319
r_angle_other_deg1.244
r_mcangle_it1.026
r_mcbond_it0.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.813
r_dihedral_angle_4_deg16.235
r_dihedral_angle_3_deg13.845
r_dihedral_angle_1_deg6.128
r_scangle_it2.67
r_scbond_it1.849
r_angle_refined_deg1.319
r_angle_other_deg1.244
r_mcangle_it1.026
r_mcbond_it0.896
r_symmetry_vdw_other0.25
r_nbd_refined0.216
r_symmetry_vdw_refined0.213
r_nbd_other0.19
r_mcbond_other0.179
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.143
r_nbtor_other0.095
r_chiral_restr0.083
r_metal_ion_refined0.02
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
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 Atoms2838
Nucleic Acid Atoms
Solvent Atoms591
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling