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Crystal structure of a/eIF2alpha-aDim2p-rRNA complex from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E3U PDB ENTRIES 2E3U AND 1YZ6 experimental model PDB 1YZ6 PDB ENTRIES 2E3U AND 1YZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 293 12% 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 coefficient Solvent content 3.92 68.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.998 α = 90 b = 93.6 β = 90 c = 116.704 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 ADSC QUANTUM 210 2006-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 24090 48
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 2E3U AND 1YZ6 2.8 50 22819 1226 99.8 0.214 0.212 0.2009 0.246 0.2326 RANDOM 28.96
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.416 r_dihedral_angle_4_deg 21.785 r_dihedral_angle_3_deg 20.111 r_dihedral_angle_1_deg 5.634 r_scangle_it 2.946 r_scbond_it 1.813 r_angle_refined_deg 1.613 r_mcangle_it 1.282 r_mcbond_it 0.749 r_angle_other_deg 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.416 r_dihedral_angle_4_deg 21.785 r_dihedral_angle_3_deg 20.111 r_dihedral_angle_1_deg 5.634 r_scangle_it 2.946 r_scbond_it 1.813 r_angle_refined_deg 1.613 r_mcangle_it 1.282 r_mcbond_it 0.749 r_angle_other_deg 0.336 r_nbtor_refined 0.32 r_nbtor_other 0.288 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.159 r_nbd_other 0.145 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.108 r_mcbond_other 0.035 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2808 Nucleic Acid Atoms 227 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling