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Structural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by Human CD38
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 6.5 300 100 mM MES, 12% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.32 46.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.937 α = 105.89 b = 53.28 β = 92.1 c = 65.919 γ = 94.81
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 2006-01-29 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 1.98 30 91.9 37397 34368 3 3
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 1.98 2.05 96.7
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 1.98 20 32092 32092 1713 100 0.21056 0.21056 0.20693 0.2119 0.27821 0.276 RANDOM 34.171
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] -0.86 0.59 0.31 0.46 0.34 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.846 r_dihedral_angle_4_deg 24.575 r_dihedral_angle_3_deg 20.04 r_dihedral_angle_1_deg 8.377 r_scangle_it 5.326 r_scbond_it 3.83 r_angle_refined_deg 2.52 r_mcangle_it 2.26 r_mcbond_it 1.486 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.846 r_dihedral_angle_4_deg 24.575 r_dihedral_angle_3_deg 20.04 r_dihedral_angle_1_deg 8.377 r_scangle_it 5.326 r_scbond_it 3.83 r_angle_refined_deg 2.52 r_mcangle_it 2.26 r_mcbond_it 1.486 r_nbtor_refined 0.32 r_nbd_refined 0.274 r_symmetry_vdw_refined 0.269 r_symmetry_hbond_refined 0.245 r_xyhbond_nbd_refined 0.216 r_chiral_restr 0.184 r_bond_refined_d 0.035 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4016 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing