Experiment: 9YUP

Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	1.0 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. \| Protein solution: 2.4 mg/mL PprA (73 uM), 150mM KCl, 20mM Tris, pH 7.5 \| Crystallization solution: 400 mM Lithium citrate, 20% (w/v) PEG 3350 \| Well solution: 1.5 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.679	α = 90
b = 123.221	β = 93.687
c = 139.288	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	PIXEL	DECTRIS PILATUS 6M	IMCA-CAT default optics (April 2017)	2017-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.976250	APS	17-ID

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	2.068	92.207	91.9	0.204	0.223	0.067	0.996	9.7	10.7		105944			36.58

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	2.068	2.409	63.2		1.775	1.936	0.605	0.588	1.9	9.8

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	2.07	41.65	1.33	103707	4886	51.51	0.2119	0.2107	0.2123	0.2361	0.2372	58.76

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	14.8721
f_angle_d	0.7866
f_chiral_restr	0.0432
f_plane_restr	0.0106
f_bond_d	0.0055

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8447
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	39

Software

Software
Software Name	Purpose
JDirector	data collection
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement