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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 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.444 α = 90 b = 57.444 β = 90 c = 107.675 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 PIXEL PSI PILATUS 6M 2007-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9794 SLS X06SA
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 50 98.1 0.06 17.4 3.9 23561 36.3
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 95.8 0.38 4.3 3.8 11086
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT Pdb entry 3D9J 2 40.76 22384 1177 99.92 0.20613 0.2044 0.23994 0.2659 RANDOM 33.719
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] 0.43 0.43 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.409 r_dihedral_angle_4_deg 16.218 r_dihedral_angle_3_deg 12.898 r_dihedral_angle_1_deg 4.563 r_scangle_it 2.333 r_scbond_it 1.585 r_angle_refined_deg 1.07 r_mcangle_it 0.932 r_mcbond_it 0.771 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.409 r_dihedral_angle_4_deg 16.218 r_dihedral_angle_3_deg 12.898 r_dihedral_angle_1_deg 4.563 r_scangle_it 2.333 r_scbond_it 1.585 r_angle_refined_deg 1.07 r_mcangle_it 0.932 r_mcbond_it 0.771 r_nbtor_refined 0.299 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.103 r_symmetry_hbond_refined 0.1 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2315 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing