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Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D9J pdb entry 3D9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.2 M Li2SO4, 1.6 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.52 α = 90 b = 57.52 β = 90 c = 106.79 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2008-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9782 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.1 50 98.8 0.06 21.6 5.1 20039 34.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 97.6 0.31 5.9 5.1 2593
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdb entry 3D9J 2.1 19.62 19235 1011 99.96 0.18357 0.18082 0.1811 0.23496 0.2293 RANDOM 35.442
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] 1.04 1.04 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.615 r_dihedral_angle_4_deg 14.305 r_dihedral_angle_3_deg 14.051 r_dihedral_angle_1_deg 4.639 r_scangle_it 2.125 r_scbond_it 1.369 r_angle_refined_deg 1.111 r_mcangle_it 0.879 r_mcbond_it 0.546 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.615 r_dihedral_angle_4_deg 14.305 r_dihedral_angle_3_deg 14.051 r_dihedral_angle_1_deg 4.639 r_scangle_it 2.125 r_scbond_it 1.369 r_angle_refined_deg 1.111 r_mcangle_it 0.879 r_mcbond_it 0.546 r_nbtor_refined 0.302 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2365 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing