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Crystal structure of the Plant Defensin NaD1 complexed with phosphatidic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.89 293.15 28% PEG 4000, 1M sodium chloride, 0.1M trisodium-citrate-citric acid, pH 5.89
Crystal Properties Matthews coefficient Solvent content 2.79 55.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.218 α = 90 b = 154.925 β = 90 c = 135.999 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 210r 2016-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.5 47.06 98.4 0.12 0.146 0.082 0.992 7.6 2.9 41102 33.58
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 2.5 2.6 99.8 0.71 0.868 0.492 0.63 2.9
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 4AAZ 2.5 44.469 1.34 41062 2042 97.72 0.2056 0.2031 0.2035 0.2519 0.2508 43.3408
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 13.093 f_angle_d 0.712 f_chiral_restr 0.048 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7380 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 475
Software Software Software Name Purpose Aimless data reduction PHASER phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building XDS data processing XDS data scaling