8BT3 | pdb_00008bt3

Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, catalytically active radical state solved by XFEL

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GP2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		294	50 mM calcium acetate, 20 mM ammonium sulphate and 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.985	α = 90
b = 46.309	β = 112.59
c = 58.514	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	CCD	RAYONIX MX340-HS		2018-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.30177	SLAC LCLS	MFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	35 (fs)			9.5 (KeV)

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	Drop on Tape	9 (µl/min)	undefined (µm)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	1.5	66.01	99.97	0.931	0.237	52.3	49.2		56800			20.48

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		0.344	0.96	1.5	19.9

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	23.82	1.34	56747	2841	99.91	0.1793	0.1775	0.1782	0.2137	0.2126	28.84

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	21.3506
f_angle_d	0.7529
f_chiral_restr	0.0459
f_bond_d	0.0056
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2518
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms

Software

Software
Software Name	Purpose
cctbx.xfel	data reduction
DIALS	data reduction
cxi.merge	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

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.