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Bacterial histone HLp from Leptospira perolatii bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB protein without DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, PH 7.5 and 25% PEG 6000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.934 α = 90 b = 67.934 β = 90 c = 97.902 γ = 90
Symmetry Space Group P 41 21 2
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 2023-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 SLS X10SA
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 2.1 43.16 99.7 0.081 0.999 11.09 5.62 13927
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 2.1 2.23 99.5 0.743 0.84 1.96 5.53
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 2.1 43.16 13229 696 99.64 0.2513 0.24983 0.2609 0.27946 0.2959 RANDOM 55.889
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] -2.74 -2.74 5.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.895 r_dihedral_angle_3_deg 18.213 r_dihedral_angle_4_deg 13.388 r_long_range_B_refined 10.499 r_long_range_B_other 10.481 r_scangle_other 6.912 r_scbond_it 4.754 r_scbond_other 4.702 r_dihedral_angle_1_deg 4.331 r_mcangle_other 4.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.895 r_dihedral_angle_3_deg 18.213 r_dihedral_angle_4_deg 13.388 r_long_range_B_refined 10.499 r_long_range_B_other 10.481 r_scangle_other 6.912 r_scbond_it 4.754 r_scbond_other 4.702 r_dihedral_angle_1_deg 4.331 r_mcangle_other 4.156 r_mcangle_it 4.152 r_mcbond_it 3.016 r_mcbond_other 3.003 r_angle_other_deg 1.457 r_angle_refined_deg 1.297 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 870 Nucleic Acid Atoms 656 Solvent Atoms 47 Heterogen Atoms 10
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement