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Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.25 293 Protein: 50 mM Tris, 150 mM NaCl, 1 mM (S)-diperodon, 10% DMSO, pH 8.0; reservoir: 100 mM Tris, 50 mM magnesium acetate, 11% PEG3350, pH 8.25
Crystal Properties Matthews coefficient Solvent content 2.18 43.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.909 α = 90 b = 66.05 β = 90 c = 107.277 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 2018-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.61 56.24 99.9 0.067 0.075 0.033 0.999 12.3 5.1 56743
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 1.61 1.67 99.8 1.528 1.714 0.765 0.466 4.8
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 5CCL 1.61 44.78 1.35 56641 2730 99.8 0.1734 0.1715 0.18 0.21 0.2138 30.1
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 22.4818 f_angle_d 1.1397 f_chiral_restr 0.0665 f_bond_d 0.0083 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3408 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing