8B0E

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VB158

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G0M

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
2.5	50.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.829	α = 90
b = 44.476	β = 97.629
c = 137.577	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 XE 16M		2021-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97624	Diamond	I03

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	39.21	96.8	0.966	2.9	5.8		70791

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			0.616

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	39.21	70705	3509	96.362	0.221	0.2198	0.2519	19.243

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]
-1.158		0.444	1.952		-0.881

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.268
r_dihedral_angle_3_deg	14.182
r_dihedral_angle_4_deg	13.063
r_dihedral_angle_1_deg	6.594
r_lrange_it	4.759
r_lrange_other	4.669
r_scangle_other	3.036
r_scangle_it	3.035
r_mcangle_it	2.331
r_mcangle_other	2.33
r_scbond_it	1.983
r_scbond_other	1.979
r_angle_refined_deg	1.584
r_mcbond_it	1.491
r_mcbond_other	1.491
r_angle_other_deg	1.399
r_nbd_refined	0.202
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.165
r_nbd_other	0.165
r_symmetry_xyhbond_nbd_refined	0.164
r_symmetry_nbd_refined	0.153
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3341
Nucleic Acid Atoms
Solvent Atoms	332
Heterogen Atoms	22

Software

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