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Structure of a minimal SF3B core in complex with spliceostatin A (form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EN4 6EN4, 5IFE experimental model PDB 5IFE 6EN4, 5IFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.17 277.15 0.1 M HEPES pH=7.17, 0.2 M MgCl2, 25% (v/v) PEG-400
Crystal Properties Matthews coefficient Solvent content 2.9 57.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.503 α = 90 b = 108.503 β = 90 c = 358.938 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 6M-F 2019-03-18 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 2.95 49.41 99.9 0.116 0.119 0.027 1 17.6 19.8 52617 119.65
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 2.95 3.04 99.7 6.113 6.275 1.403 0.402 0.6 19.6
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 6EN4, 5IFE 3 45.01 1.35 50074 2483 99.74 0.217 0.2154 0.2204 0.2468 0.2547 116.91
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 3.8251 f_angle_d 0.4984 f_chiral_restr 0.0404 f_plane_restr 0.004 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14774 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement