Experiment: 5E46

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	Native crystals of DtHNL1 were obtained by mixing 0.5ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 1 ul reservoir solution (0.9 M NaNO3; Na2HPO4; (NH4)2SO4 mix, 0.1 M Tris-Bicine Buffer pH 8.5 and 30% (w/v) polyethylene glycol monomethyl ether 550 & polyethylene glycol 20k; Morpheus condition C9). Additionally, native crystals were also grown by mixing 1 ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 0.5ul reservoir solution (0.1 M 2-(4-(2-hydroxyethyl)-1-piperazinyl) ethanesulfonic acid pH 7.5 and 10% (w/v) polyethylene glycol; JSCG condition B4). SeMet-DtHNL1 crystals were obtained in 0.2 M sodium thiocyanate, 20% (w/v) polyethylene glycol 3350. A 1:1 ratio of protein and screening solutions was used, using protein concentration of 3 mg/mL (in 10 mM Tris-HCl pH 8.0).

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.633	α = 90
b = 94.02	β = 90
c = 117.054	γ = 90

Symmetry
Space Group	I 2 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		2014-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.979	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.85	58	99.84	0.188	9.97	13.3		34750

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92	98.6		0.796	2.57	13

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	SAD	FREE R-VALUE	1.854	57.971	1.38	34748	1738	99.84	0.1567	0.1548	0.15	0.1916	0.19

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	12.57
f_angle_d	1.021
f_chiral_restr	0.046
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2749
Nucleic Acid Atoms
Solvent Atoms	467
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	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 R01GM157729.