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Crystal structure of the RK2 plasmid encoded co-complex of the C-terminally truncated transcriptional repressor protein KorB complexed with the partner repressor protein KorA bound to OA-DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QA8 experimental model PDB 2W7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 NULL
Crystal Properties Matthews coefficient Solvent content 3.12 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.253 α = 90 b = 77.095 β = 107.42 c = 84.609 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 PIXEL DECTRIS EIGER2 XE 16M 2022-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.7 82.65 100 0.13 0.135 0.039 0.993 14.1 12.4 29438 58.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 100 1.533 1.606 0.473 0.677 11.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.7 82.65 27994 1444 100 0.19402 0.191 0.1968 0.25239 0.2554 RANDOM 76.613
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] -1.59 -0.6 2.24 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.486 r_dihedral_angle_2_deg 10.653 r_long_range_B_refined 8.425 r_long_range_B_other 8.424 r_scangle_other 6.413 r_dihedral_angle_1_deg 6.216 r_mcangle_it 5.006 r_mcangle_other 5.005 r_scbond_it 4.398 r_scbond_other 4.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.486 r_dihedral_angle_2_deg 10.653 r_long_range_B_refined 8.425 r_long_range_B_other 8.424 r_scangle_other 6.413 r_dihedral_angle_1_deg 6.216 r_mcangle_it 5.006 r_mcangle_other 5.005 r_scbond_it 4.398 r_scbond_other 4.168 r_mcbond_it 3.247 r_mcbond_other 3.23 r_angle_refined_deg 1.774 r_angle_other_deg 0.52 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4942 Nucleic Acid Atoms 568 Solvent Atoms 19 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing