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Crystal structure of the FMN riboswitch bound to FMN, cobalt hexammine 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 2.78 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.156 α = 90 b = 71.156 β = 90 c = 138.421 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 1.606041 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 3.15 20 99.6 0.11 39.4 13.9 7467 7437
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 3.15 3.26 96.9 0.428 6.9 6.9 736
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 3.15 20 7069 7037 334 99.55 0.18718 0.18718 0.18499 0.1873 0.23442 0.2375 RANDOM 96.282
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] 0.23 0.12 0.23 -0.35
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.036 r_scangle_it 0.867 r_scbond_it 0.533 r_nbtor_refined 0.276 r_symmetry_hbond_refined 0.273 r_nbd_refined 0.157 r_xyhbond_nbd_refined 0.144 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.05 r_metal_ion_refined 0.026
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.036 r_scangle_it 0.867 r_scbond_it 0.533 r_nbtor_refined 0.276 r_symmetry_hbond_refined 0.273 r_nbd_refined 0.157 r_xyhbond_nbd_refined 0.144 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.05 r_metal_ion_refined 0.026 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2353 Solvent Atoms Heterogen Atoms 103
Software Software Software Name Purpose CBASS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing