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Crystal Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-B enhancer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T2K PDB ENTRY 1T2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 12%PEG 400,200mM NaCl, pH 7., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.417 α = 90 b = 46.132 β = 129.42 c = 129.325 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 109 CCD ADSC QUANTUM 210 mirrors 2006-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 2.31 50 91.7 0.027 0.027 34.8 30304 -3
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) 2.31 74.8 0.055 0.055 10.8
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 1T2K 2.31 50 28772 1530 86.11 0.18519 0.18101 0.1929 0.26433 0.2739 RANDOM 52.97
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] -2.79 -3.39 3.33 -4.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.318 r_dihedral_angle_4_deg 21.317 r_dihedral_angle_3_deg 20.234 r_dihedral_angle_1_deg 7.509 r_scangle_it 5.687 r_scbond_it 4.067 r_mcangle_it 2.563 r_angle_refined_deg 2.448 r_mcbond_it 1.559 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.318 r_dihedral_angle_4_deg 21.317 r_dihedral_angle_3_deg 20.234 r_dihedral_angle_1_deg 7.509 r_scangle_it 5.687 r_scbond_it 4.067 r_mcangle_it 2.563 r_angle_refined_deg 2.448 r_mcbond_it 1.559 r_nbtor_refined 0.315 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.228 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.127 r_symmetry_hbond_refined 0.123 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3361 Nucleic Acid Atoms 1306 Solvent Atoms 123 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing