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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 0.1 M potassium thiocyanate, 30% (w/v) PEG2000MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.296 α = 90 b = 56.296 β = 90 c = 106.739 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 2007-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9786 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 96.4 0.06 18.2 4.6 16293 42
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 90.5 0.33 4.8 4.7 1890
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 19.9 16012 848 99.95 0.19028 0.18811 0.1813 0.23102 0.2182 RANDOM 39.344
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] 1.92 1.92 -3.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.77 r_dihedral_angle_4_deg 24.717 r_dihedral_angle_3_deg 14.501 r_dihedral_angle_1_deg 5.121 r_scangle_it 2.474 r_scbond_it 1.571 r_angle_refined_deg 1.227 r_mcangle_it 0.954 r_mcbond_it 0.589 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.77 r_dihedral_angle_4_deg 24.717 r_dihedral_angle_3_deg 14.501 r_dihedral_angle_1_deg 5.121 r_scangle_it 2.474 r_scbond_it 1.571 r_angle_refined_deg 1.227 r_mcangle_it 0.954 r_mcbond_it 0.589 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_symmetry_hbond_refined 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2439 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing