☰ Navigation Tabs
Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YLS The Diels-Alder ribozyme structure from the Diels-Alder ribozyme-product complex, pdb entry 1YLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG400, sodium HEPES, magnesium chloride, ethylacetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.99 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.288 α = 90 b = 44.039 β = 106.87 c = 79.998 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 4 Si (111) double-crystal monochromator, Bent cylindrical Si-mirror (Rh coating) 2002-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 1.1 APS 14-BM-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 3.3 20 97.7 0.092 14 4.9 8607 8392
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 3.3 3.42 88.9 0.162 8 4.4
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 The Diels-Alder ribozyme structure from the Diels-Alder ribozyme-product complex, pdb entry 1YLS 3.3 20 7910 7522 388 97.7 0.22971 0.22971 0.22802 0.2413 0.26206 0.2724 RANDOM 21.884
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] 3.52 -0.82 -3.78 -0.22
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 2.597 r_angle_refined_deg 1.48 r_scbond_it 0.639 r_scangle_it 0.599 r_xyhbond_nbd_other 0.369 r_nbd_other 0.31 r_symmetry_vdw_other 0.223 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.168 r_xyhbond_nbd_refined 0.141
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 2.597 r_angle_refined_deg 1.48 r_scbond_it 0.639 r_scangle_it 0.599 r_xyhbond_nbd_other 0.369 r_nbd_other 0.31 r_symmetry_vdw_other 0.223 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.168 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.13 r_nbtor_other 0.115 r_chiral_restr 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_bond_other_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2092 Solvent Atoms Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing