8OHV | pdb_00008ohv

Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor

X-RAY DIFFRACTION

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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
2.38	48.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.037	α = 90
b = 42.614	β = 99.417
c = 140.141	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		2021-02-18	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	1.5	40.756	100	0.999	11	6.4		76979

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	1.5	1.53			0.545

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	40.756	76978	3861	99.949	0.2	0.1989	0.21	0.2231	0.23	22.124

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]
-0.264		0.532	0.871		-0.743

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.899
r_dihedral_angle_4_deg	20.262
r_dihedral_angle_3_deg	14.187
r_dihedral_angle_1_deg	6.846
r_lrange_other	5.825
r_lrange_it	5.824
r_scangle_it	4.881
r_scangle_other	4.881
r_scbond_it	3.269
r_scbond_other	3.269
r_mcangle_it	2.867
r_mcangle_other	2.867
r_mcbond_it	2.037
r_mcbond_other	2.032
r_angle_refined_deg	1.771
r_angle_other_deg	1.524
r_nbd_other	0.222
r_nbd_refined	0.212
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.14
r_symmetry_nbd_refined	0.109
r_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_chiral_restr_other	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	3417
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	17

Software

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