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Ruthenium hexammine ion interactions with Z-DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XA2 NDB ENTRY ZD0013
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 MPD, sodium cacodylate, ruthenium hexammine chloride, spermine, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.704421 51.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.953 α = 90 b = 30.821 β = 90 c = 44.596 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 293 IMAGE PLATE MARRESEARCH 2004-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.54 30 90.8 0.0526 4.7 5.04 3590 3590
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) 1.54 1.6 94.2 0.3578 1.8 4.84
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 NDB ENTRY ZD0013 1.54 25.35 3530 3276 254 90.08 0.19134 0.18923 0.1896 0.2174 0.2201 RANDOM 16.782
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] 0.12 -0.11
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 3.251 r_scangle_it 2.942 r_scbond_it 2.308 r_symmetry_hbond_refined 0.316 r_nbtor_refined 0.306 r_xyhbond_nbd_refined 0.216 r_nbd_refined 0.211 r_chiral_restr 0.148 r_symmetry_vdw_refined 0.106 r_bond_refined_d 0.028
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 3.251 r_scangle_it 2.942 r_scbond_it 2.308 r_symmetry_hbond_refined 0.316 r_nbtor_refined 0.306 r_xyhbond_nbd_refined 0.216 r_nbd_refined 0.211 r_chiral_restr 0.148 r_symmetry_vdw_refined 0.106 r_bond_refined_d 0.028 r_gen_planes_refined 0.021 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_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_it r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 252 Solvent Atoms 48 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction AMoRE phasing