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Crystal structure of the C-terminally truncated transcriptional repressor protein KorB from the RK2 plasmid complexed with CTP-gamma-S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.89 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.686 α = 90 b = 152.71 β = 90 c = 198.274 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2022-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9179 Diamond I04-1
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 2.3 198.27 100 0.236 0.245 0.067 0.997 7.9 13.3 80304
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 2.3 2.35 100 1.887 1.979 0.594 0.718 11.1
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 2.3 121.28 76214 4000 100 0.22881 0.2274 0.2278 0.25619 0.2548 RANDOM 55.721
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] 0.54 -0.97 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.229 r_dihedral_angle_2_deg 9.797 r_long_range_B_refined 6.156 r_long_range_B_other 6.154 r_dihedral_angle_1_deg 5.84 r_scangle_other 4.145 r_mcangle_it 2.958 r_mcangle_other 2.958 r_scbond_it 2.552 r_scbond_other 2.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.229 r_dihedral_angle_2_deg 9.797 r_long_range_B_refined 6.156 r_long_range_B_other 6.154 r_dihedral_angle_1_deg 5.84 r_scangle_other 4.145 r_mcangle_it 2.958 r_mcangle_other 2.958 r_scbond_it 2.552 r_scbond_other 2.542 r_mcbond_it 1.832 r_mcbond_other 1.831 r_angle_refined_deg 1.441 r_angle_other_deg 0.469 r_chiral_restr 0.071 r_bond_refined_d 0.009 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 9414 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing