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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 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.975 α = 106.08 b = 53.091 β = 91.92 c = 65.678 γ = 95.18
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 2.1 30 95.6 30854 29497 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 2.1 2.18 78.9
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 2.11 20 29500 27999 1474 94.91 0.18019 0.18019 0.17791 0.1803 0.22268 0.225 RANDOM 40.619
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] -0.96 1.79 1.51 1 2.14 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.573 r_dihedral_angle_4_deg 17.316 r_dihedral_angle_3_deg 16.017 r_dihedral_angle_1_deg 5.857 r_scangle_it 2.526 r_scbond_it 1.604 r_angle_refined_deg 1.398 r_mcangle_it 0.95 r_mcbond_it 0.595 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.573 r_dihedral_angle_4_deg 17.316 r_dihedral_angle_3_deg 16.017 r_dihedral_angle_1_deg 5.857 r_scangle_it 2.526 r_scbond_it 1.604 r_angle_refined_deg 1.398 r_mcangle_it 0.95 r_mcbond_it 0.595 r_nbtor_refined 0.306 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.099 r_symmetry_hbond_refined 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 4100 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing