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Crystal structure of histone lysine methyltransferase SmyD2 in complex with polyethylene glycol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KJK PDB entry 5KJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 PEG3350, Ethanol, Water, 1 M Tris
Crystal Properties Matthews coefficient Solvent content 3.09 60.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.84 α = 90 b = 151.84 β = 90 c = 53.74 γ = 90
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 300 mm CCD 2018-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.43 107.367 94.8 0.096 0.993 10.3 14.2 14389
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.718 72.2 0.538 0.559
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 THROUGHOUT PDB entry 5KJK 2.43 75.92 1.37 14382 753 61.5 0.1772 0.1747 0.175 0.2224 0.2232 37.8088
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 22.425 f_angle_d 1.313 f_chiral_restr 0.075 f_plane_restr 0.012 f_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3462 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 83
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing autoPROC data collection