Experiment: 4QTR

Computational design of co-assembling protein-DNA nanowires

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HHD	PDB ENTRY 3HHD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	298	800 mM, NaCl, 0.2 M Potassium thiocyanate, 20% w/v polyethylene glycerol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.098	α = 90
b = 90.098	β = 90
c = 158.923	γ = 90

Symmetry
Space Group	P 42 2 2

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		2014-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2		SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	3.1	39.2		0.022	102.5	10.7		15510

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.86	3.02	88.5		6.972		9.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	PDB ENTRY 3HHD	3.2	36.35	1.35	11351	1136	99.8	0.27	0.264	0.2788	0.322	0.3324

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	26.745
f_angle_d	1.32
f_chiral_restr	0.061
f_bond_d	0.012
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1610
Nucleic Acid Atoms	1293
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
PHENIX	refinement
DENZO	data reduction
SCALA	data scaling