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The crystal structure of a single chain H2B-H2A histone chimera from Xenopus laevis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.9 291 0.2M sodium thiocyanate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.09 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.793 α = 90 b = 44.679 β = 117.27 c = 66.45 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 CCD MARMOSAIC 225 mm CCD 2017-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 1.31 26.71 99.4 0.058 0.069 0.036 0.999 5.6 3.7 38073 13.7
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 1.31 1.39 99.8 0.892 1.052 0.55 0.619 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1KX5 1.31 20 36283 1776 99.28 0.1712 0.1695 0.1701 0.2063 0.2064 RANDOM 20.418
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] 0.47 -0.01 -0.96 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.634 r_dihedral_angle_4_deg 19.937 r_sphericity_free 14.972 r_dihedral_angle_3_deg 13.83 r_sphericity_bonded 5.968 r_dihedral_angle_1_deg 4.5 r_rigid_bond_restr 1.788 r_angle_refined_deg 1.541 r_angle_other_deg 1.057 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.634 r_dihedral_angle_4_deg 19.937 r_sphericity_free 14.972 r_dihedral_angle_3_deg 13.83 r_sphericity_bonded 5.968 r_dihedral_angle_1_deg 4.5 r_rigid_bond_restr 1.788 r_angle_refined_deg 1.541 r_angle_other_deg 1.057 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1375 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 9
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing Coot model building