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Structure of a minimal SF3B core in complex with sudemycin D6 (form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IFE 5IFE, 6EN4 experimental model PDB 6EN4 5IFE, 6EN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 0.1M Bis-tris propane pH 7.4, 0.2M KSCN, 12% (w/v) PEG-3350, 10%(v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 3.38 63.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.355 α = 90 b = 109.846 β = 90 c = 253.3 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2019-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.9 49.03 99.9 0.086 0.09 0.024 1 19.1 13.7 66573 112.16
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 2.9 2.97 98.9 4.094 4.249 1.131 0.389 0.7 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5IFE, 6EN4 3 49.03 1.34 60206 5730 99.95 0.2341 0.2324 0.2377 0.2661 0.273 112.63
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.6648 f_angle_d 0.6035 f_chiral_restr 0.043 f_plane_restr 0.005 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14812 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement