8QY1

Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylohexaose


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, 0.1 M BIS-TRIS 7.5 pH
Crystal Properties
Matthews coefficientSolvent content
2.5151.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.05α = 90
b = 78.05β = 90
c = 133.51γ = 90
Symmetry
Space GroupP 43 21 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
11.967.381000.99661.933254
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)
11.91.941000.6491

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 REPLACEMENTTHROUGHOUT1.951.0631530170699.90.195940.193720.23838RANDOM25.346
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]
1.411.41-2.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.195
r_dihedral_angle_1_deg8.477
r_dihedral_angle_2_deg8.184
r_long_range_B_refined4.417
r_long_range_B_other4.415
r_scangle_other3.417
r_mcangle_it2.861
r_mcangle_other2.86
r_scbond_it2.25
r_scbond_other2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.195
r_dihedral_angle_1_deg8.477
r_dihedral_angle_2_deg8.184
r_long_range_B_refined4.417
r_long_range_B_other4.415
r_scangle_other3.417
r_mcangle_it2.861
r_mcangle_other2.86
r_scbond_it2.25
r_scbond_other2.25
r_mcbond_it1.964
r_mcbond_other1.962
r_angle_refined_deg1.364
r_angle_other_deg0.478
r_chiral_restr0.058
r_gen_planes_refined0.008
r_bond_refined_d0.006
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 Atoms2872
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing