☰ Navigation Tabs
Crystal structure of the FMN riboswitch bound to riboflavin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 293 0.1 M Tris-HCl pH 8.4
10% PEG 4000
0.2 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.83 56.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.203 α = 90 b = 71.203 β = 90 c = 137.711 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 20 99.6 0.07 58.5 13.2 8473 8439
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 3.11 100 0.513 6 15.4 829
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 3F4E 3.01 20 8069 7850 384 97.28 0.20876 0.20876 0.20634 0.2089 0.26325 0.2572 RANDOM 72.201
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] 2.65 1.32 2.65 -3.97
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.049 r_angle_refined_deg 1.023 r_scbond_it 0.655 r_nbtor_refined 0.279 r_xyhbond_nbd_refined 0.19 r_nbd_refined 0.17 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.05 r_metal_ion_refined 0.029
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.049 r_angle_refined_deg 1.023 r_scbond_it 0.655 r_nbtor_refined 0.279 r_xyhbond_nbd_refined 0.19 r_nbd_refined 0.17 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.05 r_metal_ion_refined 0.029 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2340 Solvent Atoms Heterogen Atoms 44
Software Software Software Name Purpose CBASS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing