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Transition State Stabilization by a Catalytic RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HP6 PDB entry 1HP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 300 MPD, calcium Chloride, ammonium chloride, meta-ammonium vanadate,
pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K
Crystal Properties Matthews coefficient Solvent content 2.95 58.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 259.8 α = 90 b = 44.3 β = 107 c = 102.4 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2001-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.6 30 98.8 0.066 22 3.3 34446 34446 70.9
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) 2.6 2.69 96.4 0.608 1.7 3285
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1HP6 2.6 27.7 34442 34442 3464 98.4 0.223 0.223 0.2258 0.28 0.2801 RANDOM 93.7
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] -2.44 22.25 3.96 -1.52
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.5 c_scangle_it 12.09 c_scbond_it 9.93 c_mcangle_it 5.51 c_mcbond_it 4.14 c_improper_angle_d 1.65 c_angle_deg 1.2 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1498 Nucleic Acid Atoms 4812 Solvent Atoms 45 Heterogen Atoms 26
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing