Experiment: 5FGU

Structure of Sda1 nuclease apoprotein as an EGFP fixed-arm fusion

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JRB	EGFP component of 4JRB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	Crystals were grown by mixing 0.25uL of protein (13.3mg/mL) with 0.25uL mother liquor (45mM Na cacodylate pH 6, 13.5mM magnesium sulfate, 1.53M ammonium sulfate), using sitting drop vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.407	α = 90
b = 139.373	β = 90
c = 120.97	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93.15	CCD	RAYONIX MX300-HS		2015-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.896	50	100	0.092	25.6	7.3	54586	54586

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.896	1.93	99.6		0.61	3.54	6.4

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	EGFP component of 4JRB	1.896	38.276	1.36	54532	2733	99.56	0.178	0.1768	0.1784	0.2012	0.2004	random selection

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	13.484
f_angle_d	1.217
f_chiral_restr	0.054
f_bond_d	0.011
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3799
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	62

Software

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