2A0U

Crystal structure of the eukaryotic initiation factor 2B from Leishmania major at 2.1 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72982.1 M Sodium thiosulfate pentahydrate,0.1 M MOPS 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
238.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.733α = 90
b = 164.569β = 90
c = 172.129γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.979359SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.115.385.410.0668.72.93485625.901
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.21363.130.6281.61.63699

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.115.334856185185.410.216310.216310.213920.26378RANDOM37.77
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]
-0.551.45-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.928
r_dihedral_angle_4_deg14.599
r_dihedral_angle_3_deg12.705
r_dihedral_angle_1_deg5.725
r_scangle_it1.561
r_mcangle_it1.05
r_scbond_it1.026
r_angle_refined_deg0.989
r_mcbond_it0.681
r_nbtor_refined0.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.928
r_dihedral_angle_4_deg14.599
r_dihedral_angle_3_deg12.705
r_dihedral_angle_1_deg5.725
r_scangle_it1.561
r_mcangle_it1.05
r_scbond_it1.026
r_angle_refined_deg0.989
r_mcbond_it0.681
r_nbtor_refined0.288
r_symmetry_vdw_refined0.192
r_nbd_refined0.166
r_xyhbond_nbd_refined0.088
r_symmetry_hbond_refined0.08
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 AtomsNumber
Protein Atoms5598
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SHELXSphasing