Experiment: 9TCD

XFEL structure of oxidised Ribonucleotide reductase R2a Y122F mutant from E. coli, hexagonal P6122 form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AI8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		297	4M Sodium Formate

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.508	α = 90
b = 93.508	β = 90
c = 203.591	γ = 120

Symmetry
Space Group	P 61 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	297	CCD	RAYONIX MX340-HS		2021-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.304826	SLAC LCLS	MFX

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	2.7	22.78	97.89	0.99	20.59	1011.86		14829			62.61

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	2.7	2.79			0.93	2.27

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	2.7	22.78	1.34	14829	1482	97.89	0.2237	0.2204	0.2203	0.2538	0.2538	87.21

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	15.2328
f_angle_d	0.6181
f_chiral_restr	0.0406
f_plane_restr	0.0146
f_bond_d	0.0041

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2793
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cxi.merge	data scaling
PHENIX	phasing