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Crystal structure of C. elegans PUF-3 in complex with pos-1 RNA mut1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 3.0 ~ 3.5 M sodium formate, 0.1 M bis-tris propane pH 5.0 ~ 6.0
Crystal Properties Matthews coefficient Solvent content 7.34 83.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.152 α = 90 b = 161.152 β = 90 c = 100.013 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS EIGER X 16M 2023-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 1.0 NSLS-II 17-ID-1
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 2.4 47.08 99.75 0.147 0.159 0.06 0.997 9.2 6.91 58529 46.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99.64 0.721 0.763 1.5 6.71
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 2.4 42.18 1.33 58282 2915 99.34 0.2214 0.2202 0.2216 0.2445 0.2448 62.69
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 11.156 f_angle_d 1.1418 f_chiral_restr 0.0638 f_plane_restr 0.0111 f_bond_d 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3260 Nucleic Acid Atoms 226 Solvent Atoms 83 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing