7XTP | pdb_00007xtp

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	7D6Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1M Sodium HEPES pH7.5, 25% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.623	α = 90
b = 57.207	β = 93.951
c = 78.963	γ = 90

Symmetry
Space Group	P 1 21 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 16M		2022-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95373	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.828	46.332	99.2	0.147	11.8	7		59269			18.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.828	1.89	97.5		1.691	1.3

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	7D6Y	1.828	46.332	59269	3060	99.059	0.228	0.2263	0.23	0.2593	0.26	22.465

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]
1.332		-0.491	-0.832		-0.428

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.622
r_dihedral_angle_3_deg	12.496
r_dihedral_angle_other_3_deg	10.802
r_dihedral_angle_4_deg	10.496
r_dihedral_angle_1_deg	6.853
r_lrange_it	2.947
r_lrange_other	2.798
r_mcangle_it	1.345
r_mcangle_other	1.345
r_angle_refined_deg	1.172
r_scangle_it	1.165
r_scangle_other	1.165
r_angle_other_deg	1.134
r_mcbond_it	0.746
r_mcbond_other	0.746
r_scbond_it	0.655
r_scbond_other	0.655
r_nbd_other	0.19
r_symmetry_nbd_other	0.17
r_nbd_refined	0.167
r_nbtor_refined	0.154
r_xyhbond_nbd_refined	0.132
r_symmetry_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.1
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.041
r_bond_other_d	0.006
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4849
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	58

Software

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