8IC6

exo-beta-D-arabinanase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with Tris


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.9293.150.18 M MgCl2, 0.1 M Tris-HCl (pH 9.0), 14% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.3547.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.552α = 90
b = 97.511β = 100.55
c = 139.978γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

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
11.7548.761000.0460.0430.87414.83.417677714.64
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)
11.751.780.3660.2460.8732.9

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 REPLACEMENTTHROUGHOUT1.7548.8167894885499.950.139410.137570.17386RANDOM19.794
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]
-1.261.54-1.111.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.668
r_dihedral_angle_2_deg12.595
r_dihedral_angle_1_deg7.389
r_long_range_B_refined5.352
r_long_range_B_other5.351
r_scangle_other4.355
r_scbond_it3.188
r_scbond_other3.188
r_mcangle_it2.78
r_mcangle_other2.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.668
r_dihedral_angle_2_deg12.595
r_dihedral_angle_1_deg7.389
r_long_range_B_refined5.352
r_long_range_B_other5.351
r_scangle_other4.355
r_scbond_it3.188
r_scbond_other3.188
r_mcangle_it2.78
r_mcangle_other2.78
r_mcbond_it2.169
r_mcbond_other2.169
r_angle_refined_deg1.881
r_angle_other_deg1.327
r_chiral_restr0.102
r_gen_planes_other0.029
r_bond_refined_d0.015
r_gen_planes_refined0.014
r_bond_other_d0.002
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 Atoms13230
Nucleic Acid Atoms
Solvent Atoms1661
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing