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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 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.61 α = 90 b = 57.61 β = 90 c = 106.58 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 2007-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9538 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 1.75 100 95.3 0.04 27.7 4.6 33333 31.2
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 1.75 1.8 91.4 0.35 5.1 4.5 2588
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 1.75 19.2 32269 1721 97.23 0.18315 0.18183 0.1781 0.20723 0.2035 RANDOM 30.311
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] 0.61 0.61 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.498 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 4.31 r_scangle_it 3.266 r_scbond_it 2.044 r_mcangle_it 1.133 r_angle_refined_deg 1.129 r_mcbond_it 0.716 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.498 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 4.31 r_scangle_it 3.266 r_scbond_it 2.044 r_mcangle_it 1.133 r_angle_refined_deg 1.129 r_mcbond_it 0.716 r_nbtor_refined 0.308 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.08 r_symmetry_hbond_refined 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2357 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing