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Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to direct DNA heptad repeats
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IRQ PDB ENTRY 1IRQ AND 1CMA experimental model PDB 1CMA PDB ENTRY 1IRQ AND 1CMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 150 MM NA/KPO4, PH 7.0, 2.4 NA2MALONATE, PH 7.5, 2% AMINOCAPROIC ACID
Crystal Properties Matthews coefficient Solvent content 4 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.426 α = 90 b = 44.631 β = 108.8 c = 75.96 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 100 CCD MARRESEARCH 2004-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 2.45 30 97.4 0.06 12.7 3.3 83105 1
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 2.45 2.54 81.7 0.38 3 2.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IRQ AND 1CMA 2.45 43.44 24191 1044 97.2 0.227 0.226 0.26 0.2806 RANDOM 45.81
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] 0.88 -1.1 1.44 -3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.31 r_dihedral_angle_4_deg 21.229 r_dihedral_angle_3_deg 17.072 r_dihedral_angle_1_deg 5.761 r_scangle_it 1.426 r_angle_refined_deg 1.385 r_scbond_it 0.882 r_angle_other_deg 0.798 r_mcangle_it 0.663 r_mcbond_it 0.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.31 r_dihedral_angle_4_deg 21.229 r_dihedral_angle_3_deg 17.072 r_dihedral_angle_1_deg 5.761 r_scangle_it 1.426 r_angle_refined_deg 1.385 r_scbond_it 0.882 r_angle_other_deg 0.798 r_mcangle_it 0.663 r_mcbond_it 0.585 r_symmetry_hbond_refined 0.264 r_nbd_refined 0.214 r_nbtor_refined 0.211 r_nbd_other 0.203 r_xyhbond_nbd_refined 0.203 r_symmetry_vdw_other 0.188 r_symmetry_vdw_refined 0.181 r_nbtor_other 0.091 r_chiral_restr 0.053 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 1634 Nucleic Acid Atoms 1440 Solvent Atoms 79 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing