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Crystal structure of HERC2 ZZ domain in complex with histone H3 tail
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.933 α = 90 b = 76.439 β = 102.52 c = 33.012 γ = 90
Symmetry Space Group P 1 21 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 CMOS RDI CMOS_8M 2018-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.28 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.25 50 91 0.083 0.091 0.036 13.6 5.9 5256 29.59
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 2.25 2.33 54.7 0.157 0.184 0.093 0.963 3.2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6DS6 2.252 38.219 5192 520 90.17 0.2032 0.1985 0.2029 0.2434 0.2438 29.9424
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.114 f_angle_d 0.85 f_chiral_restr 0.047 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 904 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement autoXDS data scaling PDB_EXTRACT data extraction autoXDS data reduction MOLREP phasing