4DUM | pdb_00004dum

Co-crystal structure of eIF4E with inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	The purified protein which contained 100 uM m7-GTP was then concentrated to about 7 mg/mL in 20 mM Hepes, pH7.6, 100 mM KCl, 1mM DTT, 0.1 mM EDTA for crystallization. The m7-GTP-bound eIF4e protein was crystallized with 1:1 ratio of protein solution to reservoir solution of 17-20% PEG-3350 and 0.1-0.4M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.225	α = 90
b = 58.766	β = 90
c = 125.442	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	90	IMAGE PLATE	RIGAKU RAXIS HTC	Rigaku Varimax HR optics	2007-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54

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	2.95	62.75	98.9	0.116	9.5	2.9	18074	6282		2.9	58.7

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	2.95	3.11	97.5		0.324	2.3		765

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.95	38.236	5969	292	98.46	0.20497	0.20176	0.2	0.2711	0.27	RANDOM	35.343

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]
-0.08			1.51		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.487
r_dihedral_angle_3_deg	19.904
r_dihedral_angle_4_deg	19.663
r_dihedral_angle_1_deg	6.718
r_scangle_it	3.215
r_scbond_it	1.835
r_mcangle_it	1.581
r_angle_refined_deg	1.506
r_mcbond_it	0.818
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1547
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	40

Software

Software
Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling