☰ Navigation Tabs
Crystal Structure of the decamer CGGGCGCCCG forming a Holliday junction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P4Y PDB ID 1P4Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Drop contains 1mM DNA, 50mM buffer, 100mM MgCl2, 1mM spermine, 50% MPD in reservior , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.004 α = 90 b = 22.813 β = 116.75 c = 40.708 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 IMAGE PLATE MARRESEARCH mirrors 2008-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.9 20 97.9 0.118 0.109 2.9 3.51 1271 1239 1 64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 3 96.5 0.4579 0.4162 1 3.54 109
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 ID 1P4Y 2.94 19.81 1129 1073 56 93.15 0.2251 0.2166 0.21517 0.2125 0.23946 0.2336 RANDOM 51.104
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] 1.15 0.71 -0.97 0.46
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 5.115 r_scangle_it 4.326 r_angle_refined_deg 3.158 r_nbtor_refined 0.35 r_nbd_refined 0.274 r_symmetry_hbond_refined 0.26 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.112 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 5.115 r_scangle_it 4.326 r_angle_refined_deg 3.158 r_nbtor_refined 0.35 r_nbd_refined 0.274 r_symmetry_hbond_refined 0.26 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling