8IC6

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

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	0.18 M MgCl2, 0.1 M Tris-HCl (pH 9.0), 14% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.552	α = 90
b = 97.511	β = 100.55
c = 139.978	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 6M		2022-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.75	48.76	100	0.046	0.043	0.874	14.8	3.4		176777			14.64

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)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78			0.366	0.246	0.873	2.9

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	1.75	48.8	167894	8854	99.95	0.13941	0.13757	0.17386	RANDOM	19.794

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]
-1.26		1.54	-1.11		1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.668
r_dihedral_angle_2_deg	12.595
r_dihedral_angle_1_deg	7.389
r_long_range_B_refined	5.352
r_long_range_B_other	5.351
r_scangle_other	4.355
r_scbond_it	3.188
r_scbond_other	3.188
r_mcangle_it	2.78
r_mcangle_other	2.78
r_mcbond_it	2.169
r_mcbond_other	2.169
r_angle_refined_deg	1.881
r_angle_other_deg	1.327
r_chiral_restr	0.102
r_gen_planes_other	0.029
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
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	13230
Nucleic Acid Atoms
Solvent Atoms	1661
Heterogen Atoms	71

Software

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