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X-ray crystal structure of the M6C" riboswitch aptamer bound to 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one (PPAO)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LA5 PDB ENTRY 3LA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 3M 1,6-hexanediol, 0.1 M tris ph9.0, 0.2 M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.1 α = 90 b = 151.69 β = 90 c = 24.77 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 315 2012-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1.0 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 47.5 99.3 10992 10915 2.15 2.15
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 3LA5 2.15 47.5 1.34 10894 523 99.33 0.2064 0.2038 0.2097 0.2548 0.2597 57.4802
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.416 f_angle_d 0.91 f_chiral_restr 0.038 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1502 Solvent Atoms 22 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction PHASER phasing