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Crystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I9F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Mg Acetate, 0.05 M MES pH 5.6, 20% MPD
Crystal Properties Matthews coefficient Solvent content 2.73 54.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.347 α = 118.12 b = 51.647 β = 97.21 c = 51.972 γ = 96
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 2017-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953737 Australian Synchrotron MX2
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 2.01 44.92 97 0.055 0.074 0.049 0.995 9 2 25127
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 2.01 2.06 90.8 0.305 0.413 0.277 0.786 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5i9f 2.01 44.92 23919 1207 97.01 0.1862 0.1832 0.2476 0.254 RANDOM 32.183
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] 1.99 -1.12 -1.42 -0.06 -0.17 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.558 r_dihedral_angle_3_deg 20.49 r_dihedral_angle_4_deg 16.019 r_dihedral_angle_1_deg 11.953 r_angle_refined_deg 1.638 r_angle_other_deg 1.206 r_chiral_restr 0.078 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.558 r_dihedral_angle_3_deg 20.49 r_dihedral_angle_4_deg 16.019 r_dihedral_angle_1_deg 11.953 r_angle_refined_deg 1.638 r_angle_other_deg 1.206 r_chiral_restr 0.078 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9776 Nucleic Acid Atoms 765 Solvent Atoms 214 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing