2I2O | pdb_00002i2o

Crystal Structure of an eIF4G-like Protein from Danio rerio

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (7% PEG 4K, 0.40 M sodium chloride, 0.1 M MES/Acetate pH 5.5) CRYOPROTECTED WITH 10% PEG 4K, 0.1 M MES/Acetate pH 5.5, 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 317.796	α = 90
b = 40.948	β = 90.26
c = 40.917	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MARMOSAIC 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING SECOND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2006-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97925	APS	22-ID

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	1.92	40.612	97.5	0.074	13.377	6.4		39789

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)
	1.92	1.99	95.5		0.245	5.769	5.4	3895

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 (All)	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	SAD	THROUGHOUT	1.92	40.612	39773	1998	97.423	0.192	0.192	0.19	0.2467	0.235	0.2837	RANDOM	8.556

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]
0.771		-0.37	-0.237		-0.537

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.124
r_dihedral_angle_4_deg	21.682
r_dihedral_angle_3_deg	15.162
r_dihedral_angle_1_deg	5.853
r_scangle_it	2.991
r_scbond_it	2.001
r_angle_refined_deg	1.357
r_mcangle_it	1.1
r_mcbond_it	0.71
r_symmetry_vdw_refined	0.337
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.213
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.179
r_metal_ion_refined	0.135
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3437
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing
ARP/wARP	model building