8B0D

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VB151

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
2.38	48.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.461	α = 90
b = 43.605	β = 98.685
c = 136.202	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		2021-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	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	1.62	74.924	99.7	0.99	10.1	6		61021

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	1.62	1.65			0.516	1.1

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	1.62	74.924	61021	2969	99.577	0.199	0.1976	0.2259	36.771

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]
-0.693		3.922	0.278		-0.748

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.093
r_dihedral_angle_4_deg	16.6
r_dihedral_angle_3_deg	14.833
r_dihedral_angle_1_deg	6.554
r_lrange_it	6.463
r_lrange_other	6.451
r_scangle_other	4.949
r_scangle_it	4.945
r_mcangle_other	3.935
r_mcangle_it	3.934
r_scbond_other	3.405
r_scbond_it	3.403
r_mcbond_it	2.975
r_mcbond_other	2.971
r_angle_refined_deg	1.567
r_angle_other_deg	1.432
r_symmetry_xyhbond_nbd_refined	0.225
r_nbd_other	0.219
r_nbd_refined	0.202
r_symmetry_nbd_other	0.194
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.166
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_other	0.042
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3292
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	29

Software

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