Experiment: 6GRW

Glucuronoyl Esterase from Opitutus terrae (Au derivative)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Structure under deposition

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293.15	Reservoir composition for crystal growth: 0.03M Magnesium chloride, 0.03 M calcium chloride, 0.05M imidazole, 0.05M MES, 10% v/v MPD, 10% w/v PEG 1000, 10% v/w PEG 3500P. Heavy atom derivatization: 1.2uL crystallization mother liquor containing 0.5mM KAu(CN)2 added to drop containing crystals. Drop size and composition: Sitting drops of 0.4ul were mixed in a protein:reservoir volume ratio of 1:1 using 45 mg/mL of OtCE15A in 20 mM TRIS pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.693	α = 76.573
b = 44.608	β = 67.172
c = 50.558	γ = 70.648

Symmetry
Space Group	P 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		2017-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.979	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.5	46.27	95.9	0.042	0.05	0.999	16.69	3.55		50802			14.57

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	93.3		0.314	0.37	0.923	3.4	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	Structure under deposition	1.5	46.27	1.99	50799	2101	96.1	0.1355	0.1345	0.1585	0.1581	20.16

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.5942
f_angle_d	1.0928
f_chiral_restr	0.0764
f_plane_restr	0.0092
f_bond_d	0.0083

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3073
Nucleic Acid Atoms
Solvent Atoms	402
Heterogen Atoms	33

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
PHENIX	phasing
XSCALE	data scaling