Experiment: 9FEK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	295.15	0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4
2	VAPOR DIFFUSION, SITTING DROP	5.6	295.15	0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4
3	VAPOR DIFFUSION, SITTING DROP	5.6	295.15	0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.55
2.35	47.55
2.35	47.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.965	α = 90
b = 164.791	β = 90.03
c = 143.965	γ = 90

Symmetry
Space Group	P 1 21 1

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	Vertical CRL / Horizontal Eliptical mirror	2022-06-04	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	DECTRIS PILATUS 6M	Vertical CRL / Horizontal Eliptical mirror	2023-12-05	M	SINGLE WAVELENGTH
3	3	x-ray	100	PIXEL	DECTRIS PILATUS 6M	Vertical CRL / Horizontal Eliptical mirror	2023-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9184	ESRF	ID30B
2	SYNCHROTRON	ESRF BEAMLINE ID30B	1.48253	ESRF	ID30B
3	SYNCHROTRON	ESRF BEAMLINE ID30B	1.89289	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.58	45.01	92.89	0.1064	0.1318	0.07673	0.991	4.66	2.3		583936			22.07

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.636	85.24		1.191	1.506	0.9081	0.256	0.56	2.1

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	1.58	45.01	1.33	583176	2001	92.9	0.1999	0.1998	0.2	0.2142	0.21

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	14.52
f_angle_d	1.092
f_chiral_restr	0.065
f_plane_restr	0.013
f_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	34269
Nucleic Acid Atoms
Solvent Atoms	2815
Heterogen Atoms	144

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	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.