6Y2N

Crystal structure of ribonucleotide reductase R2 subunit solved by serial synchrotron crystallography

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Unpublished

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.5	294	16% (w/v) polyethylene glycol 3350, 2% (v/v) tacsimate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2	38.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.32	α = 90
b = 64.32	β = 90
c = 153.15	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER X 16M		2019-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.98	MAX IV	BioMAX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Silicon nitride membranes	fixed target

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	2.4	59.3	98.6	0.99	6.73	516		13245			81.8

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	2.4	2.58			0.64

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-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	Unpublished	2.4	59.3	13060	653	98.6	0.1757	0.1734	0.221	90.39

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	23.4779
f_angle_d	0.4918
f_chiral_restr	0.0354
f_plane_restr	0.0029
f_bond_d	0.0028

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2493
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
PHENIX	phasing
CrystFEL	data scaling
Coot	model building
CrystFEL	data reduction

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.