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Crystal structure of eukaryotic initiation factor 4E from Pisum sativum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IDV PDB ENTRY 2IDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 18% (W/V) PEG 3350 IN 100 MM HEPES PH 7.0 AT 293 K
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.612 α = 90 b = 136.32 β = 92.65 c = 74.415 γ = 90
Symmetry Space Group P 1 21 1
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 MIRRORS 2007-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.2 21.93 97.4 0.07 14.64 3.73 72233 -9 23.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.22 95.4 0.24 5.39 3.47
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 2IDV 2.2 136.083 72232 3642 97.205 0.183 0.1799 0.1833 0.2499 0.2497 RANDOM 23.1
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] -0.204 0.549 -1.357 1.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.342 r_dihedral_angle_4_deg 20.352 r_dihedral_angle_3_deg 16.918 r_dihedral_angle_1_deg 6.844 r_scangle_it 1.983 r_angle_refined_deg 1.481 r_scbond_it 1.258 r_mcangle_it 0.801 r_mcbond_it 0.435 r_symmetry_vdw_other 0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.342 r_dihedral_angle_4_deg 20.352 r_dihedral_angle_3_deg 16.918 r_dihedral_angle_1_deg 6.844 r_scangle_it 1.983 r_angle_refined_deg 1.481 r_scbond_it 1.258 r_mcangle_it 0.801 r_mcbond_it 0.435 r_symmetry_vdw_other 0.241 r_mcbond_other 0.09 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 Atoms Number Protein Atoms 10788 Nucleic Acid Atoms Solvent Atoms 790 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing