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Lariat-capping ribozyme with a shortened DP2 stem loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 200 mM NaCl
100 mM HEPES pH 7.5
5-25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.945 α = 90 b = 88.791 β = 90 c = 110.038 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2012-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.33 44.4 94.1 8.37 6.8 108094 87.9280042935
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3359 3.8184
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4p8z 3.33594999571 44.3955 2.00207155548 8338 418 92.6547394155 0.238474450676 0.234660832043 0.2443 0.30422432529 0.3055 77.3605845159
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.2500253813 f_angle_d 0.729209617328 f_chiral_restr 0.0356566880287 f_plane_restr 0.00310625878275 f_bond_d 0.0027074661434
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3970 Solvent Atoms Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data scaling Coot model building XDS data reduction SHELXS phasing