7D6Y | pdb_00007d6y

eIF4E in Complex with a Disulphide-Free Autonomous VH Domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V8W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	25% (w/v) PEG 6000, 0.01-02 M Ammonium Sulphate, 100mM Tris, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 198.848	α = 90
b = 45.324	β = 93.192
c = 39.763	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	PIXEL	DECTRIS EIGER X 9M		2018-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.953700	Australian Synchrotron	MX1

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	1.668	44.229	99.4	0.116	6.1	3.7		41261			3.3

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	1.67	1.76			0.673	1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2V8W	1.668	44.226	41261	2061	99.441	0.183	0.1815	0.19	0.2064	0.21	12.212

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]
0.47		-0.241	0.051		-0.491

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.413
r_dihedral_angle_4_deg	15.256
r_dihedral_angle_3_deg	11.016
r_dihedral_angle_1_deg	7.082
r_lrange_it	4.241
r_lrange_other	4.24
r_scangle_it	1.348
r_scangle_other	1.348
r_angle_other_deg	1.261
r_mcangle_it	1.241
r_mcangle_other	1.232
r_angle_refined_deg	1.197
r_scbond_it	0.786
r_scbond_other	0.786
r_mcbond_it	0.695
r_mcbond_other	0.681
r_nbd_other	0.228
r_nbd_refined	0.182
r_symmetry_nbd_other	0.174
r_symmetry_nbd_refined	0.163
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2484
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing