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RPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Co-crystallization of CID with CTD peptide occurred in a reservoir solution of 20-32% PEG3350 and 0.1M lithium sulfate. 1:3 molar ratio of protein to peptide was used
Crystal Properties Matthews coefficient Solvent content 3.15 60.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.317 α = 90 b = 90.231 β = 90 c = 135.074 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 S 6M 2022-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.5 50 92.1 0.073 0.93 5.1 3.9 13291
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 2.5 2.54 56.4 0.494 0.562 0.26 0.886 3.7
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 THROUGHOUT 2.5 42.79 1.37 13183 1320 91.1 0.2737 0.2656 0.2671 0.347 0.3467
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 21.464 f_angle_d 1.314 f_chiral_restr 0.07 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2134 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing