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Crystal structure of SR-related and CTD-associated factor 4(SCAF4-CID)with peptide S2,S5p-CTD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 25% PEG 3350, 0.2 M NH4OAc, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.718 α = 90 b = 46.923 β = 92.3 c = 139.25 γ = 90
Symmetry Space Group P 1 21 1
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 DECTRIS EIGER X 16M 2020-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 94.5 0.058 0.064 0.025 7.6 6.2 114559
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 94.8 0.756 0.829 0.334 0.813 5.8
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 MOLECULAR REPLACEMENT THROUGHOUT 3D9I 1.6 44.5 112199 2347 94.42 0.184 0.1834 0.1948 0.2104 0.2175 RANDOM 23.828
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] -0.22 -0.79 1.45 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.935 r_dihedral_angle_4_deg 22.398 r_dihedral_angle_3_deg 12.626 r_dihedral_angle_1_deg 5.262 r_angle_refined_deg 1.452 r_angle_other_deg 1.411 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.935 r_dihedral_angle_4_deg 22.398 r_dihedral_angle_3_deg 12.626 r_dihedral_angle_1_deg 5.262 r_angle_refined_deg 1.452 r_angle_other_deg 1.411 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5965 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PDB_EXTRACT data extraction MOLREP phasing