8OHT

Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with competitive inhibitor derrived from siastatin B

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PSH

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
2.54	51.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.75	α = 90
b = 44.67	β = 97.461
c = 136.268	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 PILATUS 6M		2019-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.911880	Diamond	I04-1

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	1.05	67.65	96.5	0.999	15.1	6.3		221410

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	1.05	1.07			0.582	1.4

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.05	67.648	221409	11011	96.299	0.167	0.1669	0.1774	13.041

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]
-0.273		0.227	0.505		-0.282

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.268
r_dihedral_angle_4_deg	14.875
r_dihedral_angle_3_deg	12.569
r_dihedral_angle_1_deg	6.203
r_lrange_it	4.4
r_lrange_other	4.166
r_scangle_it	3.141
r_scangle_other	3.118
r_scbond_it	2.263
r_scbond_other	2.224
r_angle_refined_deg	2.049
r_angle_other_deg	1.703
r_mcangle_it	1.658
r_mcangle_other	1.658
r_mcbond_it	1.151
r_mcbond_other	1.151
r_nbd_refined	0.251
r_symmetry_xyhbond_nbd_refined	0.229
r_xyhbond_nbd_refined	0.214
r_nbd_other	0.208
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.193
r_symmetry_nbd_refined	0.173
r_symmetry_xyhbond_nbd_other	0.137
r_chiral_restr	0.121
r_chiral_restr_other	0.111
r_symmetry_nbtor_other	0.092
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3470
Nucleic Acid Atoms
Solvent Atoms	584
Heterogen Atoms	17

Software

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