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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 1.2M Li2SO4, 1.6M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.45 α = 90 b = 56.45 β = 90 c = 106.27 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 2008-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9791 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 2.2 20 97.3 0.08 18.3 5.1 16475 36.7
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 2.2 2.3 92.6 0.33 5.3 5.1 1955
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 2.2 19.89 16046 847 99.92 0.19284 0.18976 0.1881 0.25161 0.2462 RANDOM 36.624
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] 1.62 1.62 -3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.134 r_dihedral_angle_4_deg 16.648 r_dihedral_angle_3_deg 14.596 r_dihedral_angle_1_deg 5.103 r_scangle_it 2.142 r_scbond_it 1.396 r_angle_refined_deg 1.195 r_mcangle_it 0.88 r_mcbond_it 0.539 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.134 r_dihedral_angle_4_deg 16.648 r_dihedral_angle_3_deg 14.596 r_dihedral_angle_1_deg 5.103 r_scangle_it 2.142 r_scbond_it 1.396 r_angle_refined_deg 1.195 r_mcangle_it 0.88 r_mcbond_it 0.539 r_nbtor_refined 0.304 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.082 r_symmetry_hbond_refined 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2399 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing