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yjdF riboswitch from R. gauvreauii in complex with proflavine bound to Fab BL3-6 S97N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SZU experimental model PDB 8UIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.57 52.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.873 α = 87.25 b = 75.138 β = 87.99 c = 95.727 γ = 87.72
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2018-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 95.56 95.7 0.094 0.106 0.05 0.998 8.4 4.5 32504 121.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.21 2.559 2.91 1.364 0.364 0.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.05 63.79 1.97 31354 2004 92.58 0.2272 0.2243 0.2247 0.2691 0.2691 167.08
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.6045 f_angle_d 1.1912 f_chiral_restr 0.0827 f_plane_restr 0.0107 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6646 Nucleic Acid Atoms 5340 Solvent Atoms Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALEPACK data scaling PHASER phasing