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Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 303 50 mM Na-HEPES pH 7.0, 100 mM magnesium acetate, 150 mM sodium chloride, 4% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.61 65.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.895 α = 90 b = 95.271 β = 90 c = 217.844 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 CCD ADSC QUANTUM 315 2013-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.219 32.15 98.6 0.069 0.089 0.039 14.5 4.8 30536 30536
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.22 3.39 99.7 0.542 0.542 0.695 0.302 1.4 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3IGI 3.22 32.15 28966 1540 98.1 0.1849 0.1819 0.1838 0.2418 0.2425 RANDOM 132.355
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] -0.31 0.6 -0.29
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.958 r_angle_other_deg 1.672 r_chiral_restr 0.129 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 8435 Solvent Atoms 25 Heterogen Atoms 61
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction