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Acidic residues at the active sites of CD38 and ADP-ribosyl cyclase determine NAAPD synthesis and hydrolysis activities
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YH3 PDB ENTRY 1YH3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 100 mM MES, 12% PEG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.715 α = 106.26 b = 52.823 β = 91.85 c = 65.578 γ = 95.25
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 ADSC QUANTUM 210 2005-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.976 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 30 97.1 38327 37216 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 95.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT PDB ENTRY 1YH3 1.95 20 35348 35348 1856 100 0.205 0.19807 0.19547 0.1965 0.24755 0.2479 RANDOM 45.009
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] -1.61 1.17 0.81 1.56 1.95 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.354 r_dihedral_angle_4_deg 20.57 r_dihedral_angle_3_deg 17.816 r_dihedral_angle_1_deg 6.311 r_scangle_it 3.532 r_scbond_it 2.204 r_mcangle_it 1.469 r_angle_refined_deg 1.459 r_mcbond_it 0.834 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.354 r_dihedral_angle_4_deg 20.57 r_dihedral_angle_3_deg 17.816 r_dihedral_angle_1_deg 6.311 r_scangle_it 3.532 r_scbond_it 2.204 r_mcangle_it 1.469 r_angle_refined_deg 1.459 r_mcbond_it 0.834 r_nbtor_refined 0.31 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.179 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4006 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling MOLREP phasing