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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 3D9I PDB entry 3D9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M citric acid, 2.8 M (NH4)2SO4, 1% (v/v) glycerol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.62 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.62 α = 90 b = 57.62 β = 90 c = 107.15 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 2006-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0007 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 41 97.3 0.04 24 4 44703 29.6
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 94.3 0.271 6.1 3.8 7158
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 3D9I 1.6 40.76 43194 2141 98.66 0.17987 0.17853 0.1776 0.20568 0.2063 RANDOM 30.831
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] 0.4 0.4 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.128 r_dihedral_angle_4_deg 14.655 r_dihedral_angle_3_deg 12.22 r_dihedral_angle_1_deg 4.294 r_scangle_it 3.328 r_scbond_it 2.259 r_mcangle_it 1.37 r_angle_refined_deg 1.366 r_mcbond_it 0.867 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.128 r_dihedral_angle_4_deg 14.655 r_dihedral_angle_3_deg 12.22 r_dihedral_angle_1_deg 4.294 r_scangle_it 3.328 r_scbond_it 2.259 r_mcangle_it 1.37 r_angle_refined_deg 1.366 r_mcbond_it 0.867 r_nbtor_refined 0.315 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2261 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing