8IC1

endo-alpha-D-arabinanase EndoMA1 D51N mutant from Microbacterium arabinogalactanolyticum in complex with arabinooligosaccharides


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP303.150.12 M MES-NaOH (pH 6.0), 5% PEG3000, 20% PEG200, 5 mM arabinononaose with acetonide tag
Crystal Properties
Matthews coefficientSolvent content
2.7354.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.708α = 90
b = 137.731β = 90
c = 148.589γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2021-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.846.651000.1140.0470.625126.721722820.21
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.831.2350.5280.6252

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 DIFFRACTIONSADTHROUGHOUT1.846.652061131099199.970.160740.159170.19049RANDOM22.115
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]
0.05-0.520.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.03
r_dihedral_angle_2_deg8.743
r_dihedral_angle_1_deg7.353
r_long_range_B_other5.357
r_long_range_B_refined5.356
r_scangle_other4.293
r_scbond_it2.935
r_scbond_other2.935
r_mcangle_it2.52
r_mcangle_other2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.03
r_dihedral_angle_2_deg8.743
r_dihedral_angle_1_deg7.353
r_long_range_B_other5.357
r_long_range_B_refined5.356
r_scangle_other4.293
r_scbond_it2.935
r_scbond_other2.935
r_mcangle_it2.52
r_mcangle_other2.52
r_mcbond_it1.994
r_mcbond_other1.994
r_angle_refined_deg1.581
r_angle_other_deg0.566
r_chiral_restr0.08
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d0.003
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 Atoms14836
Nucleic Acid Atoms
Solvent Atoms1314
Heterogen Atoms424

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing