8QXY

Xylanase from Bacillus circulans mutant E78Q bound to xylotriose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52915 %v/v PEGSB, 0.071 M Zn Acet, 0.1 M BIS-TRIS, 0.2 M LiSO4
Crystal Properties
Matthews coefficientSolvent content
2.6453.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.32α = 90
b = 80.32β = 90
c = 133.48γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2022-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.965459ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.443.2999.60.99310.81.885922
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)
11.41.4299.80.6061.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.4143.2976704404595.790.185690.18430.21145RANDOM21.14
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]
0.830.83-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.375
r_dihedral_angle_1_deg8.247
r_dihedral_angle_2_deg7.218
r_long_range_B_refined5.88
r_long_range_B_other5.879
r_scangle_other4.164
r_scbond_it2.843
r_scbond_other2.843
r_mcangle_other2.433
r_mcangle_it2.432
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.375
r_dihedral_angle_1_deg8.247
r_dihedral_angle_2_deg7.218
r_long_range_B_refined5.88
r_long_range_B_other5.879
r_scangle_other4.164
r_scbond_it2.843
r_scbond_other2.843
r_mcangle_other2.433
r_mcangle_it2.432
r_mcbond_it1.82
r_mcbond_other1.82
r_angle_refined_deg1.518
r_angle_other_deg0.539
r_chiral_restr0.073
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2896
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms179

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing