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Bacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CMP protein without DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium sulfate, 0.1 M sodium acetate and 22% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.56 51.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.697 α = 90 b = 34.755 β = 100.14 c = 56.433 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 2023-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 42.49 93 0.11 0.996 9.59 4.68 16780
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 95.2 0.637 0.914 2.18 4.7
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 42.49 15932 843 93 0.24959 0.24868 0.2606 0.26744 0.2847 RANDOM 39.284
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] 2.87 0.27 -2.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.107 r_dihedral_angle_4_deg 15.406 r_dihedral_angle_3_deg 14.774 r_dihedral_angle_1_deg 4.692 r_long_range_B_refined 4.484 r_long_range_B_other 4.482 r_scangle_other 1.745 r_mcangle_it 1.55 r_mcangle_other 1.549 r_angle_other_deg 1.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.107 r_dihedral_angle_4_deg 15.406 r_dihedral_angle_3_deg 14.774 r_dihedral_angle_1_deg 4.692 r_long_range_B_refined 4.484 r_long_range_B_other 4.482 r_scangle_other 1.745 r_mcangle_it 1.55 r_mcangle_other 1.549 r_angle_other_deg 1.338 r_angle_refined_deg 1.297 r_scbond_it 1.201 r_scbond_other 1.089 r_mcbond_it 0.963 r_mcbond_other 0.963 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 862 Nucleic Acid Atoms 170 Solvent Atoms 66 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing