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Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 2000 MME, LITHIUM SULFATE, SPERMIDINE, COBALT HEXAAMINE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.2 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.2 α = 90 b = 93.2 β = 90 c = 126.36 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 confocal 2005-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 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 2.65 34.01 99.5 0.07 24 11.7 9930 9889 -3 93.6
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 2.65 2.74 100 0.363 7.4 12.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 FOURIER SYNTHESIS THROUGHOUT 1X9C 2.65 34.01 -3 9930 9889 1035 0.249 0.247 0.247 0.2389 0.27 0.2517 RANDOM 55.6
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] -8.84 -5.5 -8.84 17.67
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.8 c_improper_angle_d 1.88 c_angle_deg 1.5 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1295 Solvent Atoms 9 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement CrystalClear data reduction CrystalClear data scaling CNS phasing