8QY2

Xylanase from Bacillus circulans mutant E78Q/F125A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29122.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5151.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.714α = 90
b = 78.714β = 90
c = 131.998γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2021-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.742.5899.40.99911.71.923035
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)
11.71.730.655

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 REPLACEMENTTHROUGHOUT1.742.5821750109198.320.191640.190530.2138RANDOM20.918
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]
0.630.63-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg10.674
r_dihedral_angle_1_deg8.733
r_dihedral_angle_2_deg6.274
r_long_range_B_refined6.085
r_long_range_B_other6.066
r_scangle_other4.03
r_scbond_it2.819
r_scbond_other2.817
r_mcangle_other1.999
r_mcangle_it1.998
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg10.674
r_dihedral_angle_1_deg8.733
r_dihedral_angle_2_deg6.274
r_long_range_B_refined6.085
r_long_range_B_other6.066
r_scangle_other4.03
r_scbond_it2.819
r_scbond_other2.817
r_mcangle_other1.999
r_mcangle_it1.998
r_mcbond_it1.618
r_mcbond_other1.618
r_angle_refined_deg1.476
r_angle_other_deg0.506
r_chiral_restr0.069
r_gen_planes_refined0.01
r_bond_refined_d0.008
r_bond_other_d0.001
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 Atoms127
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing