3AEV | pdb_00003aev

Crystal structure of a/eIF2alpha-aDim2p-rRNA complex from Pyrococcus horikoshii OT3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E3U	PDB ENTRIES 2E3U AND 1YZ6
experimental model	PDB	1YZ6	PDB ENTRIES 2E3U AND 1YZ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	293	12% PEG 8000, 0.1M citrate buffer, 0.2M Sodium Chloride, 6% 1,5-Diaminopentane di-HCl, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.998	α = 90
b = 93.6	β = 90
c = 116.704	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	CCD	ADSC QUANTUM 210		2006-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	50					24090			48

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 ENTRIES 2E3U AND 1YZ6	2.8	50	22819	1226	99.8	0.214	0.212	0.2	0.246	0.23	RANDOM	28.96

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]
0.65			-0.61		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.416
r_dihedral_angle_4_deg	21.785
r_dihedral_angle_3_deg	20.111
r_dihedral_angle_1_deg	5.634
r_scangle_it	2.946
r_scbond_it	1.813
r_angle_refined_deg	1.613
r_mcangle_it	1.282
r_mcbond_it	0.749
r_angle_other_deg	0.336
r_nbtor_refined	0.32
r_nbtor_other	0.288
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.159
r_nbd_other	0.145
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.108
r_mcbond_other	0.035
r_bond_refined_d	0.015
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	2808
Nucleic Acid Atoms	227
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling