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Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BNW PDB ENTRY 2BNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 120 MM NA/KPO4, PH 7.2, 2.2 M DINATRIUMMALONATE, PH 7.5, 3 % 2-METHYL-2,4-PENTANDIOL
Crystal Properties Matthews coefficient Solvent content 3.6 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.991 α = 90 b = 42.505 β = 107.17 c = 103.727 γ = 90
Symmetry Space Group P 1 21 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 2004-10-15 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 2.6 35 92.8 0.11 11.7 2.5 18516 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 2.6 2.69 72.2 0.29 3.1 1.9
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 2BNW 2.6 100 17564 944 92.8 0.227 0.225 0.232 0.258 0.2524 RANDOM 34.17
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] -1.18 2.27 0.1 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.312 r_dihedral_angle_4_deg 18.49 r_dihedral_angle_3_deg 17.026 r_dihedral_angle_1_deg 6.435 r_mcangle_it 1.051 r_angle_refined_deg 1.044 r_scangle_it 1.035 r_mcbond_it 0.878 r_angle_other_deg 0.727 r_scbond_it 0.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.312 r_dihedral_angle_4_deg 18.49 r_dihedral_angle_3_deg 17.026 r_dihedral_angle_1_deg 6.435 r_mcangle_it 1.051 r_angle_refined_deg 1.044 r_scangle_it 1.035 r_mcbond_it 0.878 r_angle_other_deg 0.727 r_scbond_it 0.554 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.209 r_nbd_refined 0.208 r_nbtor_refined 0.206 r_nbd_other 0.2 r_symmetry_vdw_other 0.181 r_symmetry_vdw_refined 0.11 r_nbtor_other 0.088 r_chiral_restr 0.051 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 1613 Nucleic Acid Atoms 927 Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing