8IC7

exo-beta-D-arabinofuranosidase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with beta-D-arabinofuranose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.9	293.15	0.2 M MgCl2, 0.1 M CHES-NaOH (pH 8.9), 14% PEG8000, 100 mM D-arabinose

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.763	α = 90
b = 97.249	β = 101.25
c = 139.681	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 2M		2022-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.35	48.62	99.9	0.056	0.036	0.988	9.5	3.4		382283			12.28

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)	Redundancy	Number Unique Reflections (All)
1	1.35	1.37			0.965	0.629	0.609	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.35	45.87	362955	19294	99.92	0.1601	0.1589	0.18244	RANDOM	17.61

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]
-0.39		1.09	-0.66		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.092
r_dihedral_angle_2_deg	9.49
r_dihedral_angle_1_deg	6.98
r_long_range_B_refined	4.65
r_long_range_B_other	4.65
r_scangle_other	3.495
r_scbond_it	2.418
r_scbond_other	2.418
r_mcangle_it	2.282
r_mcangle_other	2.282
r_angle_refined_deg	1.651
r_mcbond_it	1.617
r_mcbond_other	1.608
r_angle_other_deg	0.923
r_chiral_restr	0.089
r_gen_planes_other	0.015
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_bond_other_d	0.002
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 Atoms	Number
Protein Atoms	13226
Nucleic Acid Atoms
Solvent Atoms	1630
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing