8TCS

Structure of trehalose bound Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1

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		293	0.44 M Ammonium Chloride 21% PEG 6000 0.1 M Sodium Acetate pH 5

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.994	α = 90
b = 113.549	β = 90
c = 212.442	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 9M		2023-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0332	APS	21-ID-D

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.5	48.11	99.9	0.067	0.079	0.043	0.998	11	6.4		186241

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)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53			1.327	1.578	0.844	0.543		6.5

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	44.335	186121	9367	99.826	0.175	0.1735	0.2051	RANDOM	27

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]
-1.249			0.672		0.577

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.945
r_dihedral_angle_3_deg	13.253
r_lrange_it	6.776
r_lrange_other	6.776
r_dihedral_angle_1_deg	6.468
r_dihedral_angle_2_deg	6.241
r_scangle_it	5.481
r_scangle_other	5.48
r_scbond_it	3.929
r_scbond_other	3.928
r_angle_refined_deg	3.441
r_mcangle_other	3.099
r_mcangle_it	3.098
r_mcbond_it	2.264
r_mcbond_other	2.258
r_angle_other_deg	0.644
r_symmetry_nbd_refined	0.24
r_symmetry_xyhbond_nbd_refined	0.236
r_nbd_refined	0.235
r_nbd_other	0.197
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.187
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8610
Nucleic Acid Atoms
Solvent Atoms	867
Heterogen Atoms	100

Software

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