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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 6 300 100 mM MES, 13% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.41 49.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.35 α = 104.97 b = 53.786 β = 91.71 c = 66.826 γ = 95.04
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 2005-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.977 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 1.5 50 87 89701 78040 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.55 41.2 0.389
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 1.5 20 85572 74166 3850 86.67 0.19128 0.19128 0.18887 0.2541 0.23826 0.2871 RANDOM 40.066
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] -0.64 0.43 0.33 0.15 0.73 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.407 r_dihedral_angle_4_deg 21.199 r_dihedral_angle_3_deg 15.502 r_dihedral_angle_1_deg 5.945 r_scangle_it 4.223 r_scbond_it 2.785 r_mcangle_it 1.87 r_angle_refined_deg 1.654 r_mcbond_it 1.368 r_symmetry_vdw_refined 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.407 r_dihedral_angle_4_deg 21.199 r_dihedral_angle_3_deg 15.502 r_dihedral_angle_1_deg 5.945 r_scangle_it 4.223 r_scbond_it 2.785 r_mcangle_it 1.87 r_angle_refined_deg 1.654 r_mcbond_it 1.368 r_symmetry_vdw_refined 0.35 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.142 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 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 4076 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing