Experiment: 4YXA

Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YX7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.88	α = 90
b = 88.5	β = 116.07
c = 63.32	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r		2014-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.35	47.61	99	0.088	0.037	0.997	12.8	6.6		25759

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	99.6		0.617	0.256	0.816	2.6	6.6	2535

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4YX7	2.35	45.804	1.38	25740	1619	98.85	0.2027	0.1984	0.1994	0.2618	0.2572	46.8298

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	17.429
f_angle_d	1.464
f_chiral_restr	0.054
f_bond_d	0.011
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4810
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing