7PSK

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor GR109

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
2.47	50.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.889	α = 90
b = 44.573	β = 97.599
c = 136.897	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-F		2019-12-15	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	1.09	67.85	97.6	0.994	7.9	3.8		201068

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	1.09	1.11			0.803

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	1.09	42.383	200996	9956	97.342	0.173	0.1719	0.1849	11.154

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]
-0.334		0.162	0.366		-0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.827
r_dihedral_angle_1_deg	18.657
r_dihedral_angle_4_deg	15.322
r_dihedral_angle_3_deg	11.525
r_lrange_it	4.099
r_lrange_other	3.819
r_scangle_it	2.86
r_scangle_other	2.859
r_angle_refined_deg	1.991
r_scbond_it	1.948
r_scbond_other	1.948
r_angle_other_deg	1.692
r_mcangle_it	1.573
r_mcangle_other	1.573
r_mcbond_it	1.092
r_mcbond_other	1.089
r_symmetry_xyhbond_nbd_refined	0.281
r_nbd_refined	0.265
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.193
r_nbd_other	0.181
r_symmetry_nbd_refined	0.138
r_chiral_restr	0.115
r_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.096
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.019
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	3323
Nucleic Acid Atoms
Solvent Atoms	566
Heterogen Atoms	36

Software

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