Experiment: 7Y7O

Crystal structure of metallo-endoribonuclease YbeY from Staphylococcus aureus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		287.15	0.1 M Sodium citrate (pH 5.5), 40% (v/v) PEG 400, 1 mM Zinc sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.89	71.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.663	α = 90
b = 100.663	β = 90
c = 50.187	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS EIGER X 9M		2020-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1.28176	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.9	50	96.6	0.056	0.055	0.012	1	56	21.1		22303			17.58

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	88.7		0.184	0.194	0.044	0.988	14.6	18.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.9	43.59	1.42	22298	2002	96.53	0.1993	0.1967	0.1967	0.2256	0.2255	20.83

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	18.7362
f_angle_d	0.8994
f_chiral_restr	0.0568
f_plane_restr	0.0077
f_bond_d	0.0068

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1210
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	27

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PHENIX	phasing
HKL-2000	data scaling