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Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 PEG400, 2-methyl-2,4-pentadiol, sodium HEPES, magnesim chloride, sodium chloride, rubidium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.99 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.873 α = 90 b = 43.269 β = 106.19 c = 79.928 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 315 cylindrical platinum-coated silicon mirror 2004-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.979 NSLS X25
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 30 99.3 0.084 11.2 3.6 10784 10709
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 3.11 98.2 0.52 2.6 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 3 20 10523 9979 502 99.6 0.21 0.21006 0.20881 0.2107 0.23429 0.2334 RANDOM 23.537
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] 1.9 -1.04 -3.88 1.4
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.377 r_scbond_it 1.658 r_angle_refined_deg 1.538 r_angle_other_deg 1.44 r_xyhbond_nbd_other 0.62 r_nbd_other 0.291 r_symmetry_vdw_other 0.234 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.186 r_xyhbond_nbd_refined 0.186
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.377 r_scbond_it 1.658 r_angle_refined_deg 1.538 r_angle_other_deg 1.44 r_xyhbond_nbd_other 0.62 r_nbd_other 0.291 r_symmetry_vdw_other 0.234 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.186 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.171 r_nbtor_other 0.092 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_other 0.014 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2106 Solvent Atoms 83 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHARP phasing