3AEV

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E3UPDB ENTRIES 2E3U AND 1YZ6
experimental modelPDB 1YZ6PDB ENTRIES 2E3U AND 1YZ6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.829312% 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 coefficientSolvent content
3.9268.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.998α = 90
b = 93.6β = 90
c = 116.704γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.8502409048

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 2E3U AND 1YZ62.85022819122699.80.2140.2120.246RANDOM28.96
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.416
r_dihedral_angle_4_deg21.785
r_dihedral_angle_3_deg20.111
r_dihedral_angle_1_deg5.634
r_scangle_it2.946
r_scbond_it1.813
r_angle_refined_deg1.613
r_mcangle_it1.282
r_mcbond_it0.749
r_angle_other_deg0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.416
r_dihedral_angle_4_deg21.785
r_dihedral_angle_3_deg20.111
r_dihedral_angle_1_deg5.634
r_scangle_it2.946
r_scbond_it1.813
r_angle_refined_deg1.613
r_mcangle_it1.282
r_mcbond_it0.749
r_angle_other_deg0.336
r_nbtor_refined0.32
r_nbtor_other0.288
r_symmetry_vdw_refined0.237
r_nbd_refined0.228
r_symmetry_hbond_refined0.159
r_nbd_other0.145
r_xyhbond_nbd_refined0.139
r_chiral_restr0.108
r_mcbond_other0.035
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2808
Nucleic Acid Atoms227
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling