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Strontium bound to the Holliday junction sequence d(TCGGCGCCGA)4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NVY PDB entry 1NVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 SrCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.11 α = 90 b = 24.274 β = 110.19 c = 37.064 γ = 90
Symmetry Space Group C 1 2 1
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 OXFORD SAPPHIRE CCD multi-graded optics M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 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 2.5 16.197 99.27 0.062 5.4 1976 1975 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.565
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 PDB entry 1NVY 2.5 16.197 2325 1889 86 99.5 0.22362 0.21978 0.2198 0.30045 0.3016 RANDOM 15.878
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] -2.07 -0.08 1.95 0.06
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.678 r_angle_refined_deg 1.654 r_scbond_it 1.031 r_nbtor_refined 0.321 r_xyhbond_nbd_refined 0.235 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.175 r_metal_ion_refined 0.166 r_symmetry_vdw_refined 0.101 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.678 r_angle_refined_deg 1.654 r_scbond_it 1.031 r_nbtor_refined 0.321 r_xyhbond_nbd_refined 0.235 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.175 r_metal_ion_refined 0.166 r_symmetry_vdw_refined 0.101 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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_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 404 Solvent Atoms 50 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data collection CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing