Experiment: 9Y6E

Crystal structure of PprA from Deinococcus radiodurans in complex with DNA duplex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6BDU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	1.0 ul of pre-incubated protein-DNA solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. \| Protein-DNA solution: 5.0 mg/mL PprA (168 uM), dsDNA (100 uM), 150mM KCl, 20mM Tris, pH 7.5, 1 mM MgCl2. \| Crystallization solution (Molecular Dimensions - Morpheus 2 #2-18): 20 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4- hydroxy-L-proline, 0.1M BES, Triethanolamine (TEA), pH 7.5, 12.5% w/v PEG 4000, 20% w/v 1,2,6- Hexanetriol. \| Well solution: 1.5 M Ammonium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.427	α = 90
b = 100.427	β = 90
c = 255.598	γ = 120

Symmetry
Space Group	P 32 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 PILATUS 6M	IMCA-CAT default optics (July 2018)	2018-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.979280	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	5.79	86.972	90	0.119	0.123	0.03	0.999	13.5	16.6		4112			354.48

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	5.79	6.086	34.2		3.455	3.561	0.856	0.5	1.1	16.8

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	MOLECULAR REPLACEMENT	FREE R-VALUE	5.79	35.95	1.35	4083	197	90.65	0.272	0.2708	0.2992	0.2971	0.3431	573.79

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	16.0622
f_angle_d	0.6424
f_chiral_restr	0.0444
f_plane_restr	0.013
f_bond_d	0.0074

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8144
Nucleic Acid Atoms	615
Solvent Atoms
Heterogen Atoms

Software

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

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