9I9F | pdb_00009i9f

Crystal structure of apoform human eIF4A1 C-terminal domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZU6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	18.5% (w/v) PEG 8000, 0.2M sodium acetate trihydrate, 0.1M MES, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.97	α = 90
b = 84.97	β = 90
c = 66.42	γ = 120

Symmetry
Space Group	P 31

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 PILATUS 6M-F		2018-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	2.73	42.49	100	0.189	0.994	8.2	6.4		14242

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.73	2.78			1.375	0.507

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.731	40.003	14224	674	99.86	0.232	0.2287	0.2323	0.2937	0.2936	62.688

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]
1.372	0.686		1.372		-4.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.199
r_dihedral_angle_6_deg	14.34
r_dihedral_angle_1_deg	7.72
r_lrange_it	7.015
r_lrange_other	7.014
r_dihedral_angle_2_deg	5.35
r_mcangle_it	4.833
r_mcangle_other	4.832
r_scangle_it	4.783
r_scangle_other	4.782
r_mcbond_it	2.966
r_mcbond_other	2.966
r_scbond_it	2.91
r_scbond_other	2.909
r_angle_refined_deg	1.438
r_angle_other_deg	0.523
r_symmetry_nbd_refined	0.306
r_symmetry_xyhbond_nbd_refined	0.291
r_nbd_refined	0.241
r_symmetry_nbd_other	0.213
r_nbd_other	0.202
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.152
r_ncsr_local_group_1	0.137
r_ncsr_local_group_2	0.109
r_ncsr_local_group_3	0.09
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.07
r_xyhbond_nbd_other	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3732
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing