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Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZFR pdb entry 1ZFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 PEG550 MME, lithium sulfate, spermidine, cobalt hexamine, , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.21 70.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.49 α = 90 b = 94.49 β = 90 c = 127.58 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 83 CCD ADSC QUANTUM 210 2005-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9764 CHESS A1
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 2.4 44.3 99.2 0.043 19.1 6.25 13689 13689 -3 104.9
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) 2.4 2.48 98.7 0.43 4.3 5.91
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 pdb entry 1ZFR 2.4 44.3 -3 13643 13643 829 99.3 0.24 0.24 0.24 0.2483 0.27 0.2844 RANDOM 75.9
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] 0.95 -3.03 -15.42 14.47
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.6 c_improper_angle_d 1.73 c_angle_deg 1.5 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1309 Solvent Atoms 5 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement CrystalClear data reduction CrystalClear data scaling CNS phasing