7PSI

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum 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	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
2.45	49.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.656	α = 90
b = 44.469	β = 97.61
c = 136.714	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	1.25	74.62	98.4	0.993	6.6	3.7		133814

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	1.25	1.27			0.68

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	1.25	74.6	133776	6617	98.07	0.169	0.1685	0.1841	13.788

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]
-0.585		0.52	0.449		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.432
r_dihedral_angle_4_deg	15.297
r_dihedral_angle_3_deg	12.201
r_dihedral_angle_1_deg	6.262
r_lrange_it	4.527
r_lrange_other	4.302
r_scangle_it	3.34
r_scangle_other	3.329
r_angle_other_deg	2.388
r_scbond_it	2.298
r_scbond_other	2.203
r_mcangle_it	1.942
r_mcangle_other	1.942
r_angle_refined_deg	1.803
r_mcbond_it	1.301
r_mcbond_other	1.28
r_nbd_refined	0.212
r_symmetry_nbd_other	0.21
r_symmetry_xyhbond_nbd_refined	0.2
r_nbd_other	0.197
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.133
r_symmetry_nbd_refined	0.111
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.081
r_bond_other_d	0.036
r_gen_planes_other	0.02
r_bond_refined_d	0.016
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3458
Nucleic Acid Atoms
Solvent Atoms	466
Heterogen Atoms	23

Software

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