7PR6

Crystal structure of E. coli beta-glucuronidase in complex with covalent inhibitor ME727

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K46

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350, 0.2 M NaNO3

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.8	α = 90
b = 76.58	β = 125.01
c = 125.74	γ = 90

Symmetry
Space Group	C 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		2019-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97933	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.99	47.76	97.3	0.139	0.083	0.983	6.5	3.9		86916

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.04	98.7		1.695	0.983	0.334	0.8	3.9

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	3k46	1.99	47.803	86915	4333	96.893	0.223	0.2209	0.2631	48.325

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]
-1.766		-0.283	1.572		0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.678
r_dihedral_angle_4_deg	15.514
r_dihedral_angle_3_deg	14.33
r_dihedral_angle_1_deg	8.092
r_lrange_it	5.012
r_lrange_other	4.98
r_scangle_it	3.637
r_scangle_other	3.636
r_mcangle_it	3.06
r_mcangle_other	3.06
r_angle_other_deg	2.368
r_scbond_it	2.321
r_scbond_other	2.321
r_mcbond_it	2.005
r_mcbond_other	2.005
r_angle_refined_deg	1.716
r_symmetry_nbd_refined	0.281
r_nbd_other	0.273
r_symmetry_nbd_other	0.226
r_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.064
r_bond_other_d	0.035
r_gen_planes_other	0.016
r_bond_refined_d	0.012
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9566
Nucleic Acid Atoms
Solvent Atoms	469
Heterogen Atoms	26

Software

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