8OHX

Crystal structure of Beta-glucuronidase from Escherichia coli in complex with siastatin B derived inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PR6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		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	49.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.281	α = 90
b = 76.711	β = 102.01
c = 141.018	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		2016-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979500	Diamond	I02

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	1.95	67.04	98.4	0.997	8.1	4.1		94487

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	1.95	1.98			0.717

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	1.95	61.835	94471	4644	98.229	0.224	0.2206	0.2847	49.837

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]
-1.065		-0.735	4.979		-3.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.386
r_dihedral_angle_3_deg	16.886
r_dihedral_angle_4_deg	14.877
r_dihedral_angle_1_deg	7.995
r_lrange_it	7.331
r_lrange_other	7.325
r_scangle_it	5.404
r_scangle_other	5.404
r_mcangle_it	5.337
r_mcangle_other	5.337
r_mcbond_it	3.826
r_mcbond_other	3.826
r_scbond_it	3.666
r_scbond_other	3.666
r_angle_refined_deg	1.532
r_angle_other_deg	1.332
r_nbd_other	0.241
r_nbd_refined	0.208
r_symmetry_nbd_other	0.202
r_symmetry_nbd_refined	0.196
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.128
r_symmetry_xyhbond_nbd_other	0.125
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9538
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	24

Software

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