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Crystal Structure of Catalytic Domain of Human Phospholipase D1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 298 0.2 M ammonium citrate, 15% PEG3350, pH 5.3
Crystal Properties Matthews coefficient Solvent content 2.43 49.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.209 α = 90 b = 75.209 β = 90 c = 239.65 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 PIXEL DECTRIS EIGER X 16M 2017-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X17B1 0.97933 NSLS X17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 79.88 99 0.158 0.053 7 8.7 64302 30.221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 98.1 2.533 0.85 0.8 8.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.799 54.759 58064 1816 89.44 0.1751 0.1738 0.2145 0.2117 49.9468
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4643 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 4
Software Software Software Name Purpose xia2 data scaling PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction AutoSol phasing