1UR1

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.35M MGCL2 0.1M TRIS HCL PH6.5, 30% PEG 4K, 5% PEG 400, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
236.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.014α = 90
b = 67.7β = 90
c = 105.124γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCDTOROIDAL MIRROR2003-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.433583.30.05526.025.6249417
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)
11.431.4820.50.3341.941.38

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 1UQY1.4333.949417259383.40.1530.1510.186RANDOM10.72
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]
-0.10.11-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.622
r_dihedral_angle_3_deg14.958
r_dihedral_angle_4_deg14.711
r_dihedral_angle_1_deg6.129
r_scangle_it3.49
r_scbond_it2.279
r_angle_other_deg2.051
r_angle_refined_deg1.609
r_mcangle_it1.58
r_mcbond_it1.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.622
r_dihedral_angle_3_deg14.958
r_dihedral_angle_4_deg14.711
r_dihedral_angle_1_deg6.129
r_scangle_it3.49
r_scbond_it2.279
r_angle_other_deg2.051
r_angle_refined_deg1.609
r_mcangle_it1.58
r_mcbond_it1.041
r_symmetry_vdw_other0.289
r_mcbond_other0.254
r_symmetry_vdw_refined0.248
r_nbd_refined0.246
r_nbd_other0.213
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.169
r_nbtor_other0.121
r_chiral_restr0.098
r_metal_ion_refined0.066
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms2792
Nucleic Acid Atoms
Solvent Atoms568
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling