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Crystal structure of the FMN riboswitch bound to FMN, Cs+ soak.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES-Na pH 6.5
10% PEG 4000
0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.37 α = 90 b = 71.37 β = 90 c = 140.938 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 QUANTUM 315 2007-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.493786 APS 24-ID-C
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 3.1 20 99.4 0.121 47.3 10.8 8321 7822
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 3.1 3.21 94.3 0.629 2.9 6.4 776
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3F2Q 3.11 20 7482 7336 355 98.05 0.19332 0.19332 0.19229 0.1981 0.21456 0.2223 RANDOM 98.423
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] -1.18 -0.59 -1.18 1.76
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.058 r_scangle_it 0.728 r_scbond_it 0.433 r_nbtor_refined 0.271 r_nbd_refined 0.146 r_xyhbond_nbd_refined 0.132 r_symmetry_vdw_refined 0.112 r_chiral_restr 0.049 r_metal_ion_refined 0.034 r_symmetry_hbond_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.058 r_scangle_it 0.728 r_scbond_it 0.433 r_nbtor_refined 0.271 r_nbd_refined 0.146 r_xyhbond_nbd_refined 0.132 r_symmetry_vdw_refined 0.112 r_chiral_restr 0.049 r_metal_ion_refined 0.034 r_symmetry_hbond_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2353 Solvent Atoms 2 Heterogen Atoms 48
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling