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Crystal structure of the DEADc domain of human translation initiation factor 4A-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G9N PDB entry 2G9N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.3 291 25% PEG 3350, 0.1M Bis-Tris, 0.2M Ammonium acetate. Chymotrypsin was added to the crystallization sample at a molar ratio of approx. 1:100, pH 7.3, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.85 33.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.093 α = 90 b = 80.102 β = 90 c = 42.74 γ = 90
Symmetry Space Group P 21 21 2
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 315 2007-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97242 APS 19-ID
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 1.85 40 100 0.133 6.6 11.4 17895
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) 1.85 1.92 99.9 0.656 10.1 1744
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 (All) 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 2G9N 1.85 30 17560 883 99.57 0.187 0.187 0.185 0.1895 0.226 0.2259 RANDOM 16.434
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] -0.19 -0.18 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.249 r_dihedral_angle_4_deg 14.033 r_dihedral_angle_3_deg 12.409 r_dihedral_angle_1_deg 5.324 r_scangle_it 3.559 r_mcangle_it 3.225 r_scbond_it 2.626 r_mcbond_it 2.551 r_angle_refined_deg 1.344 r_angle_other_deg 0.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.249 r_dihedral_angle_4_deg 14.033 r_dihedral_angle_3_deg 12.409 r_dihedral_angle_1_deg 5.324 r_scangle_it 3.559 r_mcangle_it 3.225 r_scbond_it 2.626 r_mcbond_it 2.551 r_angle_refined_deg 1.344 r_angle_other_deg 0.921 r_mcbond_other 0.685 r_symmetry_vdw_other 0.232 r_nbd_refined 0.195 r_nbd_other 0.17 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.089 r_nbtor_other 0.084 r_symmetry_vdw_refined 0.072 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 1493 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection ARP/wARP model building Coot model building MolProbity model building