2JGB

Structure of human eIF4E homologous protein 4EHP with m7GTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IPBPDB ENTRY 1IPB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.520% PEG-3000, 0.1M SODIUM CITRATE PH 5.5 WITH 1MM M7GTP IN THE DROP
Crystal Properties
Matthews coefficientSolvent content
2.543

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.499α = 90
b = 49.299β = 90
c = 103.767γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2005-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.73099.60.0617.74.5111967-317.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7999.20.373.44.4

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 ENTRY 1IPB1.751.9223859126299.40.2040.2020.242RANDOM18.37
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]
0.53-0.49-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.425
r_dihedral_angle_4_deg19.504
r_dihedral_angle_3_deg13.642
r_dihedral_angle_1_deg5.991
r_scangle_it3.979
r_scbond_it2.492
r_mcangle_it1.697
r_angle_refined_deg1.494
r_mcbond_it1.153
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.425
r_dihedral_angle_4_deg19.504
r_dihedral_angle_3_deg13.642
r_dihedral_angle_1_deg5.991
r_scangle_it3.979
r_scbond_it2.492
r_mcangle_it1.697
r_angle_refined_deg1.494
r_mcbond_it1.153
r_nbtor_refined0.305
r_symmetry_vdw_refined0.231
r_nbd_refined0.209
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.106
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.006
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1665
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing