8QY3

Xylanase from Bacillus circulans mutant E78Q/F125A 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 DROP7.529122.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acetate, 0.1 M BIS-TRIS, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6453.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.838α = 90
b = 80.838β = 90
c = 131.543γ = 90
Symmetry
Space GroupI 41 2 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-10.97ESRFMASSIF-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
11.2443.1899.10.9987.91.961224
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)
11.241.260.612

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 REPLACEMENTTHROUGHOUT1.2443.1856907299196.630.197090.195410.22986RANDOM19.17
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]
0.020.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.396
r_long_range_B_other10.746
r_long_range_B_refined10.745
r_dihedral_angle_2_deg10.251
r_dihedral_angle_1_deg8.453
r_scangle_other3.535
r_scbond_it2.471
r_scbond_other2.469
r_mcangle_it2.063
r_mcangle_other2.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.396
r_long_range_B_other10.746
r_long_range_B_refined10.745
r_dihedral_angle_2_deg10.251
r_dihedral_angle_1_deg8.453
r_scangle_other3.535
r_scbond_it2.471
r_scbond_other2.469
r_mcangle_it2.063
r_mcangle_other2.063
r_angle_refined_deg1.626
r_mcbond_it1.586
r_mcbond_other1.53
r_angle_other_deg0.561
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.01
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 Atoms1442
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing