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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 PDB entry 3GC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20-30% PEG 4000, 50-250 mM AMMONIUM SULFATE, 100 MM SODIUM CACODYLATE OR SODIUM ACETATE OR MES AT PH-6.0-6.5, pH 6.0 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.205 α = 90 b = 80.029 β = 90 c = 157.725 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 130 CCD ADSC QUANTUM 315r could not see them 2007-04-25 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 1.95 78.8 90 0.084 1 2.9 110000 39086 1 1 26
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT random throughout, test set PDB entry 3GC6 1.95 40.014 1 39086 37543 2902 86.15 0.209 0.2053 0.2016 0.2515 0.2455 random
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] -5.467 1.5643 3.9028
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.888 f_angle_d 1.192 f_chiral_restr 0.079 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3753 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement PHASER phasing PHENIX model building ELVES refinement MOSFLM data reduction SCALA data scaling PHENIX phasing