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Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Unknown at 2.20 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S6E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1M potassium chloride, 15.0% polyethylene glycol monomethyl ether 5000, 0.1M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.55 51.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.283 α = 90 b = 127.283 β = 90 c = 78.864 γ = 120
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 325 mm CCD Vertical focusing mirror; double crystal Si(111) monochromator 2013-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.0 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.2 39.432 99.7 0.116 0.135 9.71 3.809 72455 -3 34.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 98 0.83 0.981 2
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 3S6E 2.2 39.432 72263 3629 99.68 0.1751 0.1744 0.1766 0.1897 0.1926 RANDOM 39.3644
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] 8.73 8.73 -17.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.92 r_dihedral_angle_4_deg 18.357 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_1_deg 5.2 r_mcangle_it 3.713 r_mcbond_it 2.282 r_mcbond_other 2.28 r_angle_refined_deg 1.635 r_angle_other_deg 1.493 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.92 r_dihedral_angle_4_deg 18.357 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_1_deg 5.2 r_mcangle_it 3.713 r_mcbond_it 2.282 r_mcbond_other 2.28 r_angle_refined_deg 1.635 r_angle_other_deg 1.493 r_chiral_restr 0.101 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.01 r_gen_planes_other 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8553 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PHASER phasing