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The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 potassium cacodylate, potassium chloride, manganese chloride
Crystal Properties Matthews coefficient Solvent content 2.49 50.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.523 α = 90 b = 110.095 β = 90 c = 182.264 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 270 2013-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 2.87 50 99.6 0.082 0.094 0.045 11.6 4.1 49349 57.79
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 2.87 2.97 100 0.5 0.574 0.278 0.803 4.2 4888
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3AV2 2.874 48.904 1.34 49288 2494 99.51 0.2208 0.2189 0.2553 0.2382 71.2038
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 26.038 f_angle_d 1.194 f_chiral_restr 0.059 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5958 Nucleic Acid Atoms 5980 Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL data scaling