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Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 2.05 angstrom junctionless ribozyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 2000 MME, lithium sulfate, cacodylate, spermidine, cobalt hexaamine, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.0
Crystal Properties Matthews coefficient Solvent content 4.4 81.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.13 α = 90 b = 91.13 β = 90 c = 144.96 γ = 120
Symmetry Space Group P 61 2 2
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 RIGAKU RAXIS IV Osmic confocal blue 2005-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.35 34.66 98.6 0.106 16.2 11.3 5532 5453 -5 63.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.35 3.47 99.1 0.51 4.7 12.4 522
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT 2.05 angstrom junctionless ribozyme 3.35 34.66 -3 5532 5450 570 98.5 0.268 0.261 0.2405 0.277 0.2379 RANDOM 94.3
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] -1.68 -19.21 -1.68 3.37
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.1 c_improper_angle_d 1.7 c_angle_deg 1.4 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.1 c_improper_angle_d 1.7 c_angle_deg 1.4 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1313 Solvent Atoms 3 Heterogen Atoms 15
Software Software Software Name Purpose CNS refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing