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Crystal structure of D60A mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C12 ceramide-1-phosphate (d18:1/12:0) at 2.55 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NT1 PDB ENTRY 4NT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 7.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.507 α = 90 b = 101.507 β = 90 c = 280.732 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 315 2010-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.55 50 98.7 0.095 12.3 3.7 18329 47.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.64 98.5 0.586 4 1786
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4NT1 2.5505 41.945 1.34 18320 1831 98.65 0.1871 0.1815 0.185 0.2363 0.2381 RANDOM 53.4689
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 13.983 f_angle_d 1.096 f_chiral_restr 0.075 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3079 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 76
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction