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Cyanide-ligated Bordetella pertussis globin coupled sensor regulatory domain S68A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294.15 10 mM Tris, 0.2 M Calcium Acetate, 10% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.958 α = 90 b = 49.702 β = 110.56 c = 67.994 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 EIGER X 16M Horizontal pre-focus bimorph mirror & KB bimorph mirrors 2023-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9793 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.85 46.67 99.48 0.026 0.992 21.1 3.4 38802 26.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.916 99.64 0.21 0.886 2 3.4
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 1.85 46.67 36907 1896 99.45 0.20855 0.20704 0.2133 0.23862 0.2492 RANDOM 27.359
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] -1.04 -0.92 1.13 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.28 r_dihedral_angle_4_deg 15.263 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 4.857 r_long_range_B_refined 2.74 r_long_range_B_other 2.711 r_scangle_other 1.448 r_mcangle_it 1.419 r_mcangle_other 1.418 r_angle_other_deg 1.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.28 r_dihedral_angle_4_deg 15.263 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 4.857 r_long_range_B_refined 2.74 r_long_range_B_other 2.711 r_scangle_other 1.448 r_mcangle_it 1.419 r_mcangle_other 1.418 r_angle_other_deg 1.169 r_angle_refined_deg 1.141 r_scbond_it 0.849 r_scbond_other 0.842 r_mcbond_it 0.813 r_mcbond_other 0.813 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3647 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing