☰ Navigation Tabs
Crystal structure of phospholipase A1, AtDSEL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.02M calcium chloride, 0.1M sodium acetate, 30% MPD
Crystal Properties Matthews coefficient Solvent content 2.97 58.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.977 α = 90 b = 95.343 β = 105.144 c = 79.278 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS EIGER X 16M 2012-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0082 Photon Factory BL-17A
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 1.799 50 99.8 0.086 35.29 7.5 105892 22.0841058546
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 1.8 1.86 0.4 4.7
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 2YIJ 1.79909514333 33.2867143454 1.35431739796 98085 4899 99.7123048146 0.179912963409 0.178279032915 0.1797 0.211731929786 0.2138 24.9417230762
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 14.2582415566 f_angle_d 1.12691161042 f_chiral_restr 0.0760831334354 f_bond_d 0.012328669973 f_plane_restr 0.00778413893933
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6409 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement