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The crystal structure of the Exon Junction Complex at 3.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FUU PDB ENTRIES 1FUU, 1FUK, AND 1P27 experimental model PDB 1FUK PDB ENTRIES 1FUU, 1FUK, AND 1P27 experimental model PDB 1P27 PDB ENTRIES 1FUU, 1FUK, AND 1P27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10% PEG 4000, 200 MM AMMONIUM ACETATE, 10 MM CACL2, NA CACODYLATE PH 6.5 .
Crystal Properties Matthews coefficient Solvent content 2.7 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.15 α = 90 b = 161.24 β = 90 c = 193.24 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 MARRESEARCH 2006-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.2 50 95.4 0.24 0.24 4.8 3.1 34926 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.4 97.2 0.68 0.68 2 3.1
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 1FUU, 1FUK, AND 1P27 3.2 46.98 33179 1747 100 0.235 0.232 0.2375 0.277 0.2819 RANDOM 66.93
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] 0.67 -0.81 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.345 r_dihedral_angle_3_deg 18.051 r_dihedral_angle_4_deg 16.657 r_dihedral_angle_1_deg 6.772 r_angle_refined_deg 1.287 r_scangle_it 1.078 r_angle_other_deg 0.815 r_mcangle_it 0.631 r_scbond_it 0.588 r_mcbond_it 0.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.345 r_dihedral_angle_3_deg 18.051 r_dihedral_angle_4_deg 16.657 r_dihedral_angle_1_deg 6.772 r_angle_refined_deg 1.287 r_scangle_it 1.078 r_angle_other_deg 0.815 r_mcangle_it 0.631 r_scbond_it 0.588 r_mcbond_it 0.387 r_nbd_refined 0.206 r_nbd_other 0.181 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.148 r_symmetry_vdw_other 0.144 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.084 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 Atoms Number Protein Atoms 10919 Nucleic Acid Atoms 242 Solvent Atoms 1 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing