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Structural insights into the catalytic mechanism of CD38: Evidence for a conformationally flexible covalent enzyme-substrate complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20-30% PEG 4000, 50-250MM AMMONIUM
SULFATE, 100 MM SODIUM CACODYLATE OR SODIUM ACETATE OR MES AT PH-6.0-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.483 α = 90 b = 80.879 β = 90 c = 151.79 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 77 CCD ADSC QUANTUM 315 2006-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 50 96.6 0.034 26 3.9 53100 53100 18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 89.3 0.306 2.91 3.4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3GC6 1.8 40.44 1 51067 51064 3873 92.8 0.1802 0.1766 0.1742 0.2231 0.2194 17.7
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] -7.07 -7.9177 -5.1526
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.531 f_angle_d 1.124 f_chiral_restr 0.081 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3831 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement PHENIX model building ELVES refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing