☰ Navigation Tabs
Crystal structure of the iminosuccinate reductase of Paracoccus denitrificans in complex with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 289 His-tagged iminosuccinate reductase (10 mg/ml) in buffer containing 25 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM MgCl2, 0.1 mM DTT, 5 mM Tb-Xo4, and 5 mM NAD+ was mixed in a ratio of 1:1 with crystallization buffer containing 200 mM Mg(NO3)2 and 20% (w/v) PEG3350 (pH 5.9).
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.386 α = 90 b = 72.407 β = 90 c = 164.266 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 PILATUS 6M-F 2019-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.56 29.4 99.9 0.097 0.105 0.041 0.998 12.6 6.5 20152 46.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.7 100 0.527 0.527 0.573 0.224 1.4 6.5
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 1OMO 2.56 29.4 1.34 20086 1998 99.92 0.1813 0.1763 0.1778 0.225 0.2273 52.24
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 20.9845 f_angle_d 0.5166 f_chiral_restr 0.3198 f_bond_d 0.0036 f_plane_restr 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4780 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 120
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHENIX phasing PHENIX refinement PDB_EXTRACT data extraction