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Structural Insight into the Sequence-Dependence of Nucleosome Positioning
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KX5 PDB ENTRY 1KX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.747 α = 90 b = 178.508 β = 102.78 c = 110.412 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 CCD MARMOSAIC 225 mm CCD 2009-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.95 60 89.7 0.069 12.4 3.7 76011
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.95 3.11 55.6 0.471 1.5 3.2 6849
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 PDB ENTRY 1KX5 2.95 60 74471 1508 89.67 0.23084 0.22947 0.2243 0.30033 0.2966 RANDOM 97.265
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] -4.22 -2.01 6.37 -3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.098 r_dihedral_angle_4_deg 18.351 r_dihedral_angle_3_deg 18.135 r_dihedral_angle_1_deg 5.175 r_scangle_it 1.444 r_angle_refined_deg 1.345 r_mcangle_it 0.953 r_scbond_it 0.76 r_mcbond_it 0.527 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.098 r_dihedral_angle_4_deg 18.351 r_dihedral_angle_3_deg 18.135 r_dihedral_angle_1_deg 5.175 r_scangle_it 1.444 r_angle_refined_deg 1.345 r_mcangle_it 0.953 r_scbond_it 0.76 r_mcbond_it 0.527 r_nbtor_refined 0.305 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12259 Nucleic Acid Atoms 12042 Solvent Atoms Heterogen Atoms 34
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling