8XZY

Structure of a xylanase Xyl-1 M4 mutant E175A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WP4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.52950.2 M sodium formate, 0.1 M Bis-Tris propane 6.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1943.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.231α = 90
b = 137.536β = 97.66
c = 52.857γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2023-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A0.99987NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.752595.80.0420.050.0260.997263.870638
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8190.40.1230.140.0650.9884.1

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 REPLACEMENTTHROUGHOUT1.7523.2967221336895.440.183010.180710.228RANDOM19.855
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]
1.11-0.44-0.05-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.725
r_dihedral_angle_4_deg15.85
r_dihedral_angle_3_deg14.875
r_dihedral_angle_1_deg8.38
r_long_range_B_refined6.049
r_long_range_B_other5.918
r_scangle_other4.438
r_scbond_it2.981
r_scbond_other2.98
r_mcangle_it2.637
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.725
r_dihedral_angle_4_deg15.85
r_dihedral_angle_3_deg14.875
r_dihedral_angle_1_deg8.38
r_long_range_B_refined6.049
r_long_range_B_other5.918
r_scangle_other4.438
r_scbond_it2.981
r_scbond_other2.98
r_mcangle_it2.637
r_mcangle_other2.637
r_mcbond_it1.899
r_mcbond_other1.895
r_angle_refined_deg1.734
r_angle_other_deg1.553
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5852
Nucleic Acid Atoms
Solvent Atoms716
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing