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Structure of tungstate bound human Phospholipase D2 catalytic domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 298 0.2M ammonium sulfate, 20% PEG3350, 0.1M bis-tris pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.09 41.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.515 α = 90 b = 132.242 β = 111.45 c = 107.089 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS 6M-F 2015-08-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.2 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.895 50 100 0.99 12.2 6.7 94443
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.895 1.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 1.895 48.55 1.35 94443 4712 99.52 0.1835 0.1824 0.1827 0.2057 0.2058
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 4.485 f_angle_d 0.608 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9343 Nucleic Acid Atoms Solvent Atoms 998 Heterogen Atoms 76
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing