Experiment: 6DGD

PriA helicase bound to dsDNA of a DNA replication fork

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NL4	4NL4 removing the winged helix domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	85 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, and 4 % glycerol
2	VAPOR DIFFUSION, HANGING DROP	5.6	293	85 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.8 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, 20 mM praseodymium III acetate hydrate
3	VAPOR DIFFUSION, HANGING DROP	5.6	293	85 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, and 0.1-0.2 mM adenosine diphosphate
4	VAPOR DIFFUSION, HANGING DROP	5.6	293	85 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, and 0.1-0.2 mM potassium chloride

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.56	α = 90
b = 106.76	β = 90
c = 256.83	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 9M		2016-11-26	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2016-11-26	M	SINGLE WAVELENGTH
3	3	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2016-06-25	M	SINGLE WAVELENGTH
4	4	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2016-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1271295	APS	21-ID-D
2	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1271295	APS	21-ID-D
3	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1271997	APS	21-ID-D
4	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1271997	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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
3	2.81	49.87	98.5	0.097	0.999	16.87	13.4		66924

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
3	2.81	2.89	80.6		3.237	0.458	0.7	10.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4NL4 removing the winged helix domain	2.823	49.343	66476	1999	98.81	0.2475	0.2506	0.2899	0.2873

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	13.636
f_angle_d	1.134
f_chiral_restr	0.065
f_bond_d	0.013
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10577
Nucleic Acid Atoms	1000
Solvent Atoms	2
Heterogen Atoms	69

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing