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Dehydration/Rehydration of a Nucleic Acid system containing a Polypyridyl Ruthenium Complex at 74% relative humidity (2/7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S80 PDB ENTRY 3S80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 1ul 1mM d(TCGGCGCCGA)2, 1ul 4mM lambda-[Ru(TAP)2(dppz)]2+, 6ul 12mM spermine, 10% MPD, 40mM sodium cacodylate, 80mM KCl, 20mM BaCl2. Equilibriated against 1ml 35% MPD, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.3 α = 90 b = 44.3 β = 90 c = 27.55 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 298 PIXEL DECTRIS 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 1.18 31.32 95.5 8969 8969 2.7
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 1.18 1.21 97.3
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 PDB ENTRY 3S80 1.18 31.32 8525 8525 424 94.56 0.09035 0.09035 0.08929 0.0895 0.11302 0.1151 RANDOM 20.251
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] -0.28 -0.28 0.55
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 52.83 r_sphericity_bonded 18.366 r_scangle_other 7.815 r_rigid_bond_restr 7.515 r_scbond_it 5.729 r_scbond_other 5.719 r_long_range_B_refined 4.225 r_long_range_B_other 4.091 r_angle_refined_deg 3.143 r_angle_other_deg 1.918
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 52.83 r_sphericity_bonded 18.366 r_scangle_other 7.815 r_rigid_bond_restr 7.515 r_scbond_it 5.729 r_scbond_other 5.719 r_long_range_B_refined 4.225 r_long_range_B_other 4.091 r_angle_refined_deg 3.143 r_angle_other_deg 1.918 r_chiral_restr 0.694 r_gen_planes_refined 0.039 r_bond_refined_d 0.022 r_gen_planes_other 0.008 r_bond_other_d 0.006 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_mcangle_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 202 Solvent Atoms 43 Heterogen Atoms 53
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling