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Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 PEG 2000 MME, lithium sulfate, cacodylate, spermidine, cobalt hexaamine, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.3 80.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.29 α = 90 b = 94.29 β = 90 c = 131.11 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 CCD ADSC QUANTUM 210 bent triangular asymmetric cut SI (111) (horizontal), RH coated SI mirror (vertical) 2005-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.977 CHESS A1
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 38.98 98.6 0.059 25.5 15.3 10537 10389 -5 84
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) 1 2.65 2.74 98.6 0.457 6 16.1 1006
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 (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 1ZFR 2.65 30.42 -3 10537 10378 640 98.4 0.199 0.196 0.1881 0.223 0.2023 RANDOM 78.7
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] -7.84 -4.13 -7.84 15.67
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17.1 c_improper_angle_d 1.69 c_angle_deg 1.3 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1295 Solvent Atoms 14 Heterogen Atoms 20
Software Software Software Name Purpose CNS refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing