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Crystal structure of wild type human CD38 in complex with NAADP and ADPRP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YH3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 0.1M sodium acetate pH 4.0, 15% PEG 10K, 0.2M ammonium acetate, 3% isopropanol, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.848 α = 110.35 b = 53.683 β = 91.42 c = 63.38 γ = 94.53
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 MX225 2009-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97623 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.69 100 95 0.079 17.2 7.1 53940
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 1.7 1.76 68.5 0.213 4.3 3904
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 1YH3 1.69 50 53915 2718 94.14 0.1679 0.1664 0.1747 0.1948 0.2028 RANDOM 31.0308
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] -1.12 -0.06 0.08 0.4 0.45 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.896 r_dihedral_angle_4_deg 13.669 r_dihedral_angle_3_deg 12.033 r_dihedral_angle_1_deg 5.57 r_angle_refined_deg 1.209 r_angle_other_deg 0.867 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.896 r_dihedral_angle_4_deg 13.669 r_dihedral_angle_3_deg 12.033 r_dihedral_angle_1_deg 5.57 r_angle_refined_deg 1.209 r_angle_other_deg 0.867 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4058 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 66
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction