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Structure of a minimal SF3B core in complex with pladienolide D (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 7.63, PEG-3350 11%, Glycerol 15%, KSCN 0.2M
Crystal Properties Matthews coefficient Solvent content 3.35 63.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.075 α = 90 b = 109.799 β = 90 c = 251.936 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 PILATUS 6M-F 2019-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.023 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 2.81 50.33 100 0.091 0.095 0.026 0.999 16.5 12.9 72883 98.39
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 2.81 2.87 99.6 2.635 2.747 0.767 0.474 1 12.6
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 50.33 1.18 59705 5628 99.95 0.2124 0.2102 0.2213 0.255 0.2607 96.3
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 23.6057 f_angle_d 0.5652 f_chiral_restr 0.0423 f_plane_restr 0.0041 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14733 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement