3HKS | pdb_00003hks

Crystal structure of eukaryotic translation initiation factor eIF-5A2 from Arabidopsis thaliana

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X6O	PDB ENTRY 1x6o

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	25% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.56	α = 90
b = 79.83	β = 90
c = 94.95	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	IMAGE PLATE	MAR scanner 345 mm plate		2005-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.23	94.92	99.5	0.066				20393

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.23	2.28

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 (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	PDB ENTRY 1x6o	2.3	94.92	18539	1183	99.78	0.20435	0.20201	0.2	0.24074	0.23	RANDOM	21.554

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]
-1.21			1.66		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.2
r_dihedral_angle_4_deg	22.012
r_dihedral_angle_3_deg	15.588
r_dihedral_angle_1_deg	6.245
r_scangle_it	3.533
r_scbond_it	2.127
r_mcangle_it	1.315
r_angle_refined_deg	1.266
r_mcbond_it	1.224
r_nbtor_refined	0.293
r_symmetry_hbond_refined	0.221
r_symmetry_vdw_refined	0.202
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2163
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	24

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling