7F07 | pdb_00007f07

Autonomous VH domain that interacts with eIF4E at the Capped mRNA Binding site.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BEA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M TRIS.HCl pH 8.5 25% (v/v) PEG 550 MME

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.522	α = 90
b = 81.819	β = 90
c = 122.987	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS EIGER X 9M		2018-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95372	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	2.25	40.996	100	0.12	4.7	13.4		19226

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	2.25	2.37	100		0.755	1	12.8

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	4BEA	2.25	40.943	19171	976	99.969	0.217	0.2145	0.22	0.266	0.27	48.131

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]
-2.942			8.55		-5.608

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.574
r_dihedral_angle_3_deg	17.256
r_dihedral_angle_4_deg	15.616
r_dihedral_angle_1_deg	7.437
r_lrange_it	7.098
r_lrange_other	7.091
r_scangle_it	5.01
r_scangle_other	5.01
r_mcangle_it	4.452
r_mcangle_other	4.451
r_scbond_it	3.011
r_scbond_other	3.01
r_mcbond_it	2.86
r_mcbond_other	2.858
r_angle_refined_deg	1.311
r_angle_other_deg	1.165
r_symmetry_nbd_refined	0.238
r_nbd_other	0.227
r_symmetry_nbd_other	0.182
r_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.158
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.055
r_chiral_restr	0.051
r_gen_planes_refined	0.005
r_bond_refined_d	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	2490
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms

Software

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