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Human nucleosome core particle with H2A.X S139E variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291.15 potassium chloride, manganese chloride, potassium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.95 α = 90 b = 109.46 β = 90 c = 183.38 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 98.15 PIXEL DECTRIS PILATUS 2M 2014-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.2 93.99 98.6 0.066 0.082 0.035 0.995 11.6 5.4 109157 73.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 91.2 0.735 3.3
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 3ut9 2.2 93.2 106763 2154 98.41 0.2323 0.2315 0.2361 0.2745 0.2755 RANDOM 67.573
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] 0.26 -3.07 2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.436 r_dihedral_angle_3_deg 19.718 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_1_deg 6.437 r_angle_refined_deg 1.492 r_angle_other_deg 1.436 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.436 r_dihedral_angle_3_deg 19.718 r_dihedral_angle_4_deg 18.545 r_dihedral_angle_1_deg 6.437 r_angle_refined_deg 1.492 r_angle_other_deg 1.436 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6192 Nucleic Acid Atoms 5939 Solvent Atoms 72 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing