7PSJ

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VL166

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.393	α = 90
b = 44.117	β = 97.579
c = 136.708	γ = 90

Symmetry
Space Group	I 1 2 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 EIGER2 X 16M		2020-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979499	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.55	75.11	99.9	0.997	7.1	3.9		71878

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58			0.793

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5g0m	1.55	75.112	71856	3593	99.796	0.196	0.1946	0.2227	21.816

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]
-1.535		0.684	3.605		-2.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.61
r_dihedral_angle_4_deg	16.476
r_dihedral_angle_3_deg	13.328
r_dihedral_angle_1_deg	6.689
r_lrange_it	5.329
r_lrange_other	5.236
r_scangle_it	3.799
r_scangle_other	3.798
r_mcangle_other	2.576
r_mcangle_it	2.574
r_angle_other_deg	2.527
r_scbond_it	2.497
r_scbond_other	2.497
r_mcbond_it	1.752
r_mcbond_other	1.729
r_angle_refined_deg	1.643
r_symmetry_nbd_other	0.213
r_symmetry_xyhbond_nbd_refined	0.209
r_nbd_refined	0.206
r_chiral_restr	0.2
r_nbd_other	0.198
r_symmetry_nbd_refined	0.191
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.08
r_bond_other_d	0.036
r_gen_planes_other	0.014
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_symmetry_xyhbond_nbd_other	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3312
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	32

Software

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