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HsNMT1 in complex with both MyrCoA and Acetylated-GKSFSKPR peptide reveals N-terminal Lysine Myristoylation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 22% PEG8K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.818 α = 90 b = 178.442 β = 90 c = 58.271 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2019-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.984002 SOLEIL PROXIMA 1
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 1.9 48.79 99.9 0.102 0.106 0.028 0.999 15.4 14.2 131286 27.4485684842
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 1.9 1.94 99.7 0.941 0.975 0.252 0.934 14.6
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 THROUGHOUT 5O9T 1.90000651019 48.787531993 0.373714053464 124981 6205 99.8649620455 0.174280163469 0.171966781113 0.1761 0.219991662291 0.2229 31.6244340982
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 15.8779025149 f_angle_d 0.857558441095 f_chiral_restr 0.0560073882315 f_bond_d 0.00627128189972 f_plane_restr 0.00603939379583
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6406 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 144
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction