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Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome
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 85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.348 α = 90 b = 109.785 β = 90 c = 182.424 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 MARMOSAIC 225 mm CCD 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.89 SLS X06SA
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 2.75 76.5 95.8 0.085 21.2 6.8 53707
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) 1 2.75 2.9 89.5 0.425 3.6 6.5 7216
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 2.75 38.19 52580 1078 95.38 0.22324 0.2225 0.2219 0.25904 0.2569 RANDOM 54.531
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] 1.36 -2.8 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.624 r_dihedral_angle_4_deg 20.164 r_dihedral_angle_3_deg 16.676 r_dihedral_angle_1_deg 4.932 r_scangle_it 2.138 r_angle_refined_deg 1.475 r_scbond_it 1.322 r_mcangle_it 1.317 r_mcbond_it 0.687 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.624 r_dihedral_angle_4_deg 20.164 r_dihedral_angle_3_deg 16.676 r_dihedral_angle_1_deg 4.932 r_scangle_it 2.138 r_angle_refined_deg 1.475 r_scbond_it 1.322 r_mcangle_it 1.317 r_mcbond_it 0.687 r_nbtor_refined 0.312 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.082 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 6156 Nucleic Acid Atoms 6021 Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling