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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 3.2 M (NH4)2SO4, 1% (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.53 α = 90 b = 57.53 β = 90 c = 106.39 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 1.0001 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 1.6 40 98.2 0.05 20.7 5.7 44673 25.4
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 1.6 1.7 94.9 0.413 4.8 5 7175
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 1.6 37.99 43320 2150 99.93 0.17348 0.17206 0.1716 0.20111 0.1988 RANDOM 26.403
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] 0.52 0.52 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.904 r_dihedral_angle_4_deg 18.395 r_dihedral_angle_3_deg 12.508 r_dihedral_angle_1_deg 4.001 r_scangle_it 3.116 r_scbond_it 2.006 r_angle_refined_deg 1.269 r_mcangle_it 1.216 r_mcbond_it 0.768 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.904 r_dihedral_angle_4_deg 18.395 r_dihedral_angle_3_deg 12.508 r_dihedral_angle_1_deg 4.001 r_scangle_it 3.116 r_scbond_it 2.006 r_angle_refined_deg 1.269 r_mcangle_it 1.216 r_mcbond_it 0.768 r_nbtor_refined 0.315 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2402 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing