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Structure of the S-adenosylhomocysteine riboswitch at 2.18 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NPN PDB ENTRY 3NPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7 293 2.25 mM Spermine, 9 mM magnesium chloride, 0.9 mM spermidine, 2.5 mM Cobalt(III)hexammine chloride, 0.05 M sodium cacodylate pH 7.0, 5% (v/v) PEG 400, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.18 61.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.793 α = 90 b = 103.241 β = 97.9 c = 69.583 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 100 CCD ADSC QUANTUM 315 2009-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25
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 1.95 23.014 86.4 0.071 6.2 41336
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) 1.95 2.05 47 1.005 1.005 1.157 0.566 0.7 4 3268
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3NPN 2.1814 23.014 0.03 32745 1761 95.74 0.2358 0.2353 0.2272 0.2454 0.2331
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] -7.1324 0.2297 5.5823 0.646
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.42 f_angle_d 0.536 f_chiral_restr 0.033 f_bond_d 0.001 f_plane_restr 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3235 Solvent Atoms 575 Heterogen Atoms 183
Software Software Software Name Purpose SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction CBASS data collection MOSFLM data reduction