Experiment: 6NIE

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	1:1 volume of protein solution (10 mg/mL BesD, lysine (1.5 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (MES pH 6.5 (100 mM), sodium chloride (0.6 mM), containing 20% (v/v) PEG 4000. Soaked anaerobically in a solution containing (NH4)2Fe(SO4)2 * 6H2O (1mM), alpha-ketoglutarate (1 mM), sodium ascorbate (1 mM), lysine (1 mM), and glycerol (20% (v/v) for 30 min before flash freezing in liquid nitrogen

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.11

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 61.358	�� = 115.36
b = 68.916	�� = 91.57
c = 79.702	�� = 112.95

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	194	PIXEL	DECTRIS PILATUS3 S 6M		2018-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.95	70.03	97.35	0.998	10.7	13.6		149915

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	95.7		0.78

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.95	70.027	1.96	149912	7295	97.35	0.1791	0.1772	0.2159

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	18.977
f_angle_d	0.982
f_chiral_restr	0.058
f_bond_d	0.01
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7808
Nucleic Acid Atoms
Solvent Atoms	847
Heterogen Atoms	89

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	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.