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Lambda-[Ru(TAP)2(11-Cl-dppz)] with a DNA decamer at atomic resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 291 1mM d(TCGGCGCCGA)2, 3mM [Ru(TAP)2(11-Cl-dppz)]2Cl, 40mM sodium cacodylate pH 6.3, 12mM spermine, 80mM KCl, 20mM BaCl2, 10% 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.92 57.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.34 α = 90 b = 42.34 β = 90 c = 39.63 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2012-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.8266 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.02 28.95 100 18496 18496 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.02 1.05 99.5
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 (All) 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 3QRN 1.02 28.93 17529 17529 946 97.88 0.10202 0.10142 0.10142 0.0984 0.11391 0.1139 RANDOM 17.878
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] -1.28 -1.28 2.56
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 28.455 r_sphericity_bonded 15.716 r_rigid_bond_restr 6.891 r_angle_refined_deg 2.34 r_angle_other_deg 1.57 r_chiral_restr 0.087 r_gen_planes_refined 0.039 r_bond_refined_d 0.02 r_gen_planes_other 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 28.455 r_sphericity_bonded 15.716 r_rigid_bond_restr 6.891 r_angle_refined_deg 2.34 r_angle_other_deg 1.57 r_chiral_restr 0.087 r_gen_planes_refined 0.039 r_bond_refined_d 0.02 r_gen_planes_other 0.008 r_bond_other_d 0.003 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 202 Solvent Atoms 81 Heterogen Atoms 53
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling