☰ Navigation Tabs
Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 273 50 mM Tris pH 8.2, 10 mM MgCl2, 32% MPD, 0.9 M KCl, 0.5 mM spermine 2 mM NH4VO3
Crystal Properties Matthews coefficient Solvent content 4.25 71.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.251 α = 90 b = 87.419 β = 90 c = 105.539 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 300 mm CCD 2014-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.501 APS 21-ID-D
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 2.95 50 99.4 0.196 139.7 6.3 12773
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3 97.2 0.636 19.4 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5DI2 3.201 27.429 1.37 11830 1180 98.82 0.2499 0.2471 0.2469 0.2777 0.2811
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.199 f_angle_d 1.251 f_chiral_restr 0.054 f_plane_restr 0.009 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1456 Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing