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Crystal structure of a F. nucleatum FMN riboswitch - Free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F2Q PDB ENTRY 3F2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 RNA WAS CRYSTALLIZED FROM 11% PEG-4000, 0.32 M MGCL2, AND 0.01 M TRIS-CL, PH 8.4
Crystal Properties Matthews coefficient Solvent content 2.91 64.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.472 α = 90 b = 73.472 β = 90 c = 135.168 γ = 120
Symmetry Space Group P 31 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 CCD 2009-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 3.3 40 98.1 0.09 22.9 5.9 6627 2 113.49
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 3.3 3.42 90.1 0.48 2.8 4
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3F2Q 3.298 29.844 6383 356 94.52 0.2087 0.2058 0.2037 0.2572 0.2536 132.3
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] -5.4284 -5.4284 9.2468
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.898 f_angle_d 0.517 f_chiral_restr 0.053 f_plane_restr 0.036 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2374 Solvent Atoms 26 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling CNS phasing