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Crystal structure of C. elegans PUF-3 in complex with RNA II-3
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 7.31 83.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.774 α = 90 b = 160.774 β = 90 c = 99.55 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 2023-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.8 33.95 99.7 0.167 0.182 0.071 0.997 8 6.47 36703
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 2.8 2.9 0.925 0.763 1.2
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 2.8 33.94 1.35 36357 1833 98.76 0.2484 0.2473 0.2476 0.2707 0.2716 89.69
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 12.3518 f_angle_d 1.231 f_chiral_restr 0.0774 f_bond_d 0.0081 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3210 Nucleic Acid Atoms 246 Solvent Atoms 20 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing