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Crystal structure of the FMN riboswitch bound to FMN, Mn2+ 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 MES-Na pH 6.5
10% PEG 4000
0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.988 α = 90 b = 70.988 β = 90 c = 140.004 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 2008-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.5498 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 3.2 20 99.5 0.073 39.2 8.6 7144 7108
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 3.2 3.31 95.5 0.339 4 6.7 687
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 3.2 20 6783 6750 329 99.52 0.1938 0.1938 0.19179 0.2002 0.23721 0.2319 RANDOM 109.237
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] -3.59 -1.8 -3.59 5.39
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.019 r_scangle_it 0.953 r_scbond_it 0.543 r_nbtor_refined 0.272 r_nbd_refined 0.142 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.135 r_symmetry_vdw_refined 0.121 r_metal_ion_refined 0.055 r_chiral_restr 0.046
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.019 r_scangle_it 0.953 r_scbond_it 0.543 r_nbtor_refined 0.272 r_nbd_refined 0.142 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.135 r_symmetry_vdw_refined 0.121 r_metal_ion_refined 0.055 r_chiral_restr 0.046 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 Heterogen Atoms 48
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling