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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 9QT0 protein without DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Carboxylic acids, 0.1 M Morpheus Buffer System 3, pH 8.5 and 50% (v/v) Morpheus Precipitant Mix 4
Crystal Properties Matthews coefficient Solvent content 1.71 28.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.769 α = 90 b = 91.613 β = 90 c = 100.33 γ = 90
Symmetry Space Group F 2 2 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 2023-06-11 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 1.9 39.56 68.4 0.06 1 13.86 7.51 6179
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 1.9 2.05 20 1.534 0.426 1.34 6.44
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 1.9 39.56 5261 918 68.35 0.24269 0.23492 0.2391 0.28794 0.2881 RANDOM 45.919
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] 0.33 0.28 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.567 r_dihedral_angle_4_deg 17.549 r_dihedral_angle_3_deg 13.195 r_long_range_B_refined 5.373 r_long_range_B_other 5.365 r_scangle_other 4.09 r_dihedral_angle_1_deg 4.041 r_mcangle_it 2.608 r_mcangle_other 2.608 r_scbond_it 2.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.567 r_dihedral_angle_4_deg 17.549 r_dihedral_angle_3_deg 13.195 r_long_range_B_refined 5.373 r_long_range_B_other 5.365 r_scangle_other 4.09 r_dihedral_angle_1_deg 4.041 r_mcangle_it 2.608 r_mcangle_other 2.608 r_scbond_it 2.587 r_scbond_other 2.585 r_mcbond_it 1.775 r_mcbond_other 1.767 r_angle_other_deg 1.35 r_angle_refined_deg 1.173 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 429 Nucleic Acid Atoms 305 Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction STARANISO data scaling MOLREP phasing REFMAC refinement