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Crystal structure of engineered phospholipase D mutant superPLD 2-48
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V0Y PDB entry 1V0Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.4 291 21% PEG8000, 0.15 M lithium sulfate, citrate-NaOH, pH 4.4
Crystal Properties Matthews coefficient Solvent content 2.01 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.828 α = 90 b = 73.254 β = 90 c = 87.19 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2021-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 1.85 56.09 99.15 0.998 13.55 13.1 40025 28.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.918 0.879 2.35
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 PDB entry 1V0Y 1.85 56.09 1.36 40025 1957 99.15 0.1751 0.1729 0.173 0.2174 0.2174 36.66
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 6.5433 f_angle_d 1.0686 f_chiral_restr 0.0619 f_plane_restr 0.0103 f_bond_d 0.0102
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3631 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing Coot model building