Experiment: 6DGD

X-RAY DIFFRACTION

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	R-Free	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	0.2899

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.