☰ Navigation Tabs
Crystal structure of PDE4D catalytic domain complexed with 33a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 0.1 M Hepes (pH 7.4), 0.1 M MgCl2, 15% PEG3350, 10% isopropanol, 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.25 45.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.294 α = 90 b = 80.834 β = 90 c = 163.423 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 CCD Bruker AXIOM 200 2021-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.1 24.19 99.47 0.099 17.4 5.2 45663 17.3909484335
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 2.1 2.2 100 0.212 5.1 4.2
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 NONE 5WQA 2.10002940118 24.1887843961 1.37956347377 45654 2245 99.4488857908 0.198836690932 0.196501567225 0.1967 0.24396145707 0.2438 22.8378426616
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 18.9960656834 f_angle_d 0.937769685126 f_chiral_restr 0.0472311328241 f_bond_d 0.0058509822639 f_plane_restr 0.00413851306616
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5235 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction