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Crystal structure of the KH1 domain of human RNA-binding E3 ubiquitin-protein ligase MEX-3C complex with RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 5% v/v Tacsimate pH 7.0, 0.1M HEPES pH 7.0, 10% w/v polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.366 α = 90 b = 76.366 β = 90 c = 36.392 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 ADSC QUANTUM 315r 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
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 1.8 40 99.6 0.159 0.168 0.053 3.6 10.1 11406 22.96
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 1.8 1.86 98.9 0.705 0.742 0.229 0.865 10.3 1130
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DGR 1.798 38.183 1.41 11402 564 99.49 0.1738 0.172 0.2091 0.2124 26.3348
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 15.672 f_angle_d 0.778 f_chiral_restr 0.049 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 735 Nucleic Acid Atoms 125 Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data scaling MOSFLM data reduction PHASER phasing HKL data scaling