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The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site
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 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 3.95 68.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.35 α = 90 b = 93.35 β = 90 c = 123.56 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) MONOCHROMATOR, RH-COATED SI MIRROR 2004-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 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 2.38 47 99.2 0.036 29.9 8.7 13252 -5 70.8
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) 2.38 2.47 99.9 0.429 5.2 8.5
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 PDB ENTRY 1ZFR 2.38 46.68 -5 13252 13267 1367 99.5 0.237 0.237 0.2342 0.257 0.2429 RANDOM 69.9
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] -9.5 -7.8 -9.5 19
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 16.5 c_scangle_it 4.037 c_mcangle_it 2.992 c_scbond_it 2.148 c_improper_angle_d 1.79 c_mcbond_it 1.547 c_angle_deg 1.3 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1308 Solvent Atoms 21 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement ADSC data collection CrystalClear data scaling CNS phasing