9I9G | pdb_00009i9g

Crystal structure of human eIF4A1 C-terminal domain in complex with hippuristanol

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		eIF4A1 C-terminal domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	20 % (w/v) PEG 6000, 0.2 M sodium chloride, 0.1 M sodium acetate, pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.199	α = 77.093
b = 32.974	β = 74.669
c = 37.781	γ = 81.044

Symmetry
Space Group	P 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 PILATUS3 6M		2018-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	1.7	35.76	97	0.06	0.997	14.2	3.3		15055

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	1.7	1.73			0.173	0.967

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	1.7	35.002	15049	771	97.003	0.151	0.1489	0.1623	0.1896	0.1977	14.507

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]
0.202	0.055	-0.114	-0.583	0.29	0.381

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.605
r_dihedral_angle_3_deg	15.406
r_dihedral_angle_2_deg	8.466
r_dihedral_angle_1_deg	6.841
r_lrange_it	5.755
r_lrange_other	5.754
r_scangle_it	4.077
r_scangle_other	4.075
r_scbond_it	2.644
r_scbond_other	2.642
r_mcangle_it	2.371
r_mcangle_other	2.37
r_angle_refined_deg	1.775
r_mcbond_it	1.53
r_mcbond_other	1.529
r_chiral_restr_other	1.125
r_angle_other_deg	0.732
r_xyhbond_nbd_refined	0.265
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.197
r_symmetry_nbd_refined	0.19
r_nbd_other	0.19
r_nbtor_refined	0.178
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1354
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	33

Software

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