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Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Mg2+ bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HHN PDB ENTRY 3HHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 50 mM sodium cacodylate, pH 6.0, 20 mM calcium chloride, 10 mM strontium chloride, 1 mM spermine, 26% MPD, crystals were crushed and used as microseeding stocks, calcium chloride was replaced with magnesium chloride prior to freezing, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.19 α = 99.86 b = 70.237 β = 99.34 c = 71.214 γ = 103.81
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 315 2009-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.125 40 99.1 0.135 6.5 7.2 18739 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.2 98.1 0.469 5.4 918
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 PDB ENTRY 3HHN 3.125 37.9073 18730 964 98.67 0.1974 0.1965 0.2398 0.2367 RANDOM 76.199
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] -1.294 -3.251 7.469 -0.062 -0.719 1.356
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.197 f_nbd_refined 4.086 f_angle_d 1.327 f_chiral_restr 0.055 f_bond_d 0.007 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1475 Nucleic Acid Atoms 5862 Solvent Atoms 51 Heterogen Atoms 46
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing