3JUI | pdb_00003jui

Crystal Structure of the C-terminal Domain of Human Translation Initiation Factor eIF2B epsilon Subunit

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.7	289	PEG8000, Calcium acetate, Sodium Cocadylate, pH 7.7, vapor diffusion, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.537	α = 90
b = 66.082	β = 90
c = 136.128	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210	mirrors	2008-11-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.9796, 0.9794, 0.9600	NSLS	X12C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	50	90.6	0.07	13.2	7.2		13260

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	84.1		0.313		7.4	1196

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	29.16	13149	661	90.21	0.214	0.211	0.21	0.279	0.21	RANDOM	24.42

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.704
r_dihedral_angle_4_deg	20.742
r_dihedral_angle_3_deg	16.909
r_dihedral_angle_1_deg	5.87
r_scangle_it	4.448
r_scbond_it	3.19
r_mcangle_it	1.812
r_angle_refined_deg	1.761
r_mcbond_it	1.1
r_chiral_restr	0.146

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.704
r_dihedral_angle_4_deg	20.742
r_dihedral_angle_3_deg	16.909
r_dihedral_angle_1_deg	5.87
r_scangle_it	4.448
r_scbond_it	3.19
r_mcangle_it	1.812
r_angle_refined_deg	1.761
r_mcbond_it	1.1
r_chiral_restr	0.146
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1422
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.