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Porcine Dihydropyrimidine dehydrogenase (DPD) complexed with 5-Ethynyluracil (5EU) - Open Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H7X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Drops were formed by mixing 3 uL of 39 uM of DPD, 1 mM 5EU, 1 mM NADPH in 25 mM HEPES, 10 mM DTT, 10% glycerol pH 7.5 with 3 uL of well solution (1 mL) containing 50-200 mM NaCl, 19% PEG 6000, 1 mM DTT pH 4.8
Crystal Properties Matthews coefficient Solvent content 2.4 48.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.031 α = 90 b = 160.046 β = 95.95 c = 164.074 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 100 CCD MARMOSAIC 225 mm CCD 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 1.127 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.99 50 90.2 0.172 0.211 0.121 0.992 5.6 2.9 255614
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.02 66 0.869 0.665 0.377 1.1 2.1
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 THROUGHOUT 1H7X 2 45.62 1.34 219153 10691 77.1 0.1749 0.1721 0.1727 0.2286 0.2286 30.5255
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 30769 Nucleic Acid Atoms Solvent Atoms 2171 Heterogen Atoms 504
Software Software Software Name Purpose xia2 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction