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Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FAX
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 3.77 67.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.89 α = 90 b = 95.24 β = 90 c = 227.896 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 PIXEL DECTRIS PILATUS 6M-F 2013-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979500 APS 24-ID-C
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 3.279 48.893 99.9 0.074 0.089 0.035 15.8 6.5 30804 30804
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 3.28 3.46 99.8 0.995 0.995 1.197 0.467 0.8 6.5
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 4FAX 3.28 48.89 29194 1550 99.78 0.1983 0.1967 0.192 0.2296 0.2254 RANDOM 132.249
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] 2.69 -4.61 1.92
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.792 r_angle_other_deg 1.66 r_chiral_restr 0.113 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 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 8390 Solvent Atoms 25 Heterogen Atoms 63
Software Software Software Name Purpose XDS data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing