5W2F

Crystal Structure of the C-terminal Domain of Human eIF2D at 1.4 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	3.5 M Sodium Formate, 100 mM Sodium Acetate pH4.5

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.65	α = 90
b = 50.65	β = 90
c = 183.653	γ = 90

Symmetry
Space Group	P 43 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	100	PIXEL	DECTRIS PILATUS 6M-F		2016-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.00	APS	24-ID-C

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	1.4	48.83	99.1	0.043	0.049	0.023	0.999	14.7	4.2		47791

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	1.4	1.42	94.2		1.098	1.297	0.674	0.5		3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.4	48.83	45498	2259	98.65	0.1419	0.1404	0.1718	RANDOM	29.529

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]
0.37			0.37		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.095
r_dihedral_angle_2_deg	37.651
r_sphericity_bonded	14.981
r_dihedral_angle_4_deg	12.333
r_dihedral_angle_3_deg	10.966
r_dihedral_angle_1_deg	4.952
r_rigid_bond_restr	1.506
r_angle_refined_deg	1.346
r_angle_other_deg	0.913
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.095
r_dihedral_angle_2_deg	37.651
r_sphericity_bonded	14.981
r_dihedral_angle_4_deg	12.333
r_dihedral_angle_3_deg	10.966
r_dihedral_angle_1_deg	4.952
r_rigid_bond_restr	1.506
r_angle_refined_deg	1.346
r_angle_other_deg	0.913
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1581
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
SHELX	data reduction
SHELXDE	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 R01GM133198.