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Crystal structure of the FMN riboswitch bound to FMN, split RNA.
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 2.92 57.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.471 α = 90 b = 71.471 β = 90 c = 140.554 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 2008-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.08 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 3.05 20 99.3 0.061 60.7 16.4 8337 8297
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 3.05 3.16 98.6 0.511 8.2 15.8 813
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 3.05 20 7953 7869 382 98.94 0.20105 0.20105 0.19955 0.1993 0.23176 0.2322 RANDOM 63.051
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] 2.69 1.34 2.69 -4.03
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.472 r_angle_refined_deg 1.028 r_scbond_it 0.886 r_nbtor_refined 0.281 r_xyhbond_nbd_refined 0.173 r_nbd_refined 0.172 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.142 r_metal_ion_refined 0.074 r_chiral_restr 0.053
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.472 r_angle_refined_deg 1.028 r_scbond_it 0.886 r_nbtor_refined 0.281 r_xyhbond_nbd_refined 0.173 r_nbd_refined 0.172 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.142 r_metal_ion_refined 0.074 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2340 Solvent Atoms 2 Heterogen Atoms 45
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling