9DTS | pdb_00009dts

Crystal structure of the human eIF4A1/AMPPNP/amidino-rocaglate/polypurine RNA complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ZC9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	290	0.2 M ammonium acetate, 8% PEG20000, 10% Hampton Silver Bullet Reagent B5 (0.33% w/v 2,7-naphthalenedisulfonic acid disodium salt, 0.33% w/v azelaic acid, 0.33% w/v trans-cinnamic acid, 0.02 M HEPES sodium pH 6.8)

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.11	α = 95.22
b = 87.314	β = 105.29
c = 93.159	γ = 108.35

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	100	PIXEL	DECTRIS EIGER X 9M		2023-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.920105	NSLS-II	17-ID-1

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	1.689	81.362	96	0.09	0.11	0.061	0.993	5.61	3		201775

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	1.69	1.75	91.16		1.18	1.45	0.84	0.368		2.7

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	1.69	40.68	1.96	201757	1999	95.99	0.2033	0.2029	0.2034	0.2402	0.2404	40.02

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	10.609
f_angle_d	1.2678
f_chiral_restr	0.0674
f_plane_restr	0.0193
f_bond_d	0.0122

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12035
Nucleic Acid Atoms	720
Solvent Atoms	899
Heterogen Atoms	292

Software

Software
Software Name	Purpose
autoPROC	data processing
PHENIX	phasing
PHENIX	model building
PHENIX	refinement

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.