Experiment: 9OR6

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	1.5 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: 5.0 mg/mL PprA (168 uM), 43bp dsDNA (101 uM), 150mM KCl, 20mM Tris, pH 7.5, 1 mM MgCl2. \| Crystallization solution (Molecular Dimensions - Morpheus 2 #94): 10 mM Spermine tetrahydrochloride, 10 mM Spermidine trihydrochloride, 10 mM 1,4 Diaminobutane dihydrochloride, 10 mM DL Ornithine monohydrochloride 0.1M Gly-Gly, AMPD, pH 8.5, 13% w/v PEG 4000, 21% w/v 1,2,6 Hexanetriol. \| Well solution: 2.0 M Ammonium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.486	α = 90
b = 34.083	β = 98.337
c = 98.734	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 6M	CMCF-ID optics setup	2019-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97934	CLSI	08ID-1

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	2.9	90.774	96.2	0.094	0.13	0.069	0.993	9.6	3.3		13352			51.01

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	2.904	2.954	100		0.443	0.61	0.417	0.756	2.4	3.4

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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.9	90.77	1.35	13350	650	96.21	0.2276	0.2266	0.2479	0.226	51.11

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	17.1593
f_angle_d	0.6416
f_chiral_restr	0.0428
f_plane_restr	0.0063
f_bond_d	0.0037

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3993
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	30

Software

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