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Dehydration/Rehydration of a Nucleic Acid system containing a Polypyridyl Ruthenium Complex at 97% relative humidity (3/7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QRN PDB ENTRY 3QRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING 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. Crystal was rehydrated to 97% relative humidity on the beamline using the HC1b., pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.99 58.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.98 α = 90 b = 42.98 β = 90 c = 39.42 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 1.6 30.39 88.6 4564 4564 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 1.6 1.64 91.3
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 3QRN 1.6 30.39 4341 4341 210 87.07 0.14646 0.14646 0.14516 0.1368 0.17432 0.1624 RANDOM 29.108
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] -0.07 -0.07 0.13
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.429 r_long_range_B_other 5.359 r_scangle_other 4.173 r_angle_refined_deg 2.995 r_scbond_it 2.803 r_scbond_other 2.799 r_angle_other_deg 1.661 r_chiral_restr 0.067 r_gen_planes_refined 0.026 r_bond_refined_d 0.017
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.429 r_long_range_B_other 5.359 r_scangle_other 4.173 r_angle_refined_deg 2.995 r_scbond_it 2.803 r_scbond_other 2.799 r_angle_other_deg 1.661 r_chiral_restr 0.067 r_gen_planes_refined 0.026 r_bond_refined_d 0.017 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 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 202 Solvent Atoms 33 Heterogen Atoms 52
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling