☰ Navigation Tabs
Crystal structure of Crocodile defensin CpoBD13:phosphatidic acid complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7T9Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.8M Sodium phosphate monobasic monohydrate, 0.8M Potassium phosphate monobasic, 0.1M sodium HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.83 32.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.056 α = 90.093 b = 33.694 β = 90.016 c = 36.642 γ = 90.014
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 EIGER2 S 16M 2020-08-28 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) 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 1.45 24.82 99.9 0.081 0.99 6.5 2.5 21344 9.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 90.3 0.652 0.416 2 2.5
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 7T9Q 1.45 24.78 1.96 21267 916 92.74 0.195 0.1941 0.1958 0.2151 0.2197 17.84
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 17.1261 f_angle_d 1.0637 f_chiral_restr 0.06 f_bond_d 0.0062 f_plane_restr 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1264 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 109
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing