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Crystal structure of the FMN riboswitch bound to FMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Ir data
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% PEG4000
0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.832 α = 90 b = 70.832 β = 90 c = 141.146 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 2008-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.97949 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 2.95 20 99 0.052 67 16.3 9187 9095
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 2.95 3.06 100 0.57 5.3 14.4 879
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 Ir data 2.95 20 8625 8619 431 99.93 0.20151 0.20151 0.19952 0.1946 0.24335 0.2511 RANDOM 66.742
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] 4.66 2.33 4.66 -7
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.532 r_angle_refined_deg 1.007 r_scbond_it 0.94 r_nbtor_refined 0.286 r_nbd_refined 0.184 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_refined 0.118 r_symmetry_hbond_refined 0.084 r_chiral_restr 0.05 r_metal_ion_refined 0.038
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.532 r_angle_refined_deg 1.007 r_scbond_it 0.94 r_nbtor_refined 0.286 r_nbd_refined 0.184 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_refined 0.118 r_symmetry_hbond_refined 0.084 r_chiral_restr 0.05 r_metal_ion_refined 0.038 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2353 Solvent Atoms 2 Heterogen Atoms 47
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling