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Lariat-capping ribozyme (circular permutation form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG 3,350 or (ii) 0.2 Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.63 α = 90 b = 85.71 β = 90 c = 108.53 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 2012-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.6 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 2.5 47.83 96.5 3.16 7 34663 46.1964978861
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 2.50003617357 2.589
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 4p9r 2.50003617357 47.8244954657 1.59236930785 34663 1968 96.5032434088 0.200698514255 0.198171132345 0.1981 0.244903584028 0.243 45.2999933522
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 13.582135344 f_angle_d 0.520596296905 f_chiral_restr 0.0228738097266 f_plane_restr 0.00243759276119 f_bond_d 0.00164361938429
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 4054 Solvent Atoms 88 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling SHELX phasing