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Crystal structure of human CD38 in complex with compound CZ-48
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 pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG 10000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.914 α = 65.21 b = 50.847 β = 83.6 c = 68.617 γ = 82.52
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 RAYONIX MX-225 2010-05-08 M SINGLE WAVELENGTH 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97908 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 2.04 50 97.9 0.069 11.1 3.5 31537
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 2.04 2.12 96.8 0.384 3.4 3108
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1YH3 2.04 50 31515 1583 97.18 0.1851 0.1829 0.2273 0.2591 RANDOM 38.506
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] -0.42 -0.28 -0.67 -0.52 0.75 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.145 r_dihedral_angle_4_deg 14.892 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 5.305 r_scangle_it 2.255 r_scbond_it 1.429 r_angle_refined_deg 1.088 r_angle_other_deg 0.799 r_mcangle_it 0.797 r_mcbond_it 0.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.145 r_dihedral_angle_4_deg 14.892 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 5.305 r_scangle_it 2.255 r_scbond_it 1.429 r_angle_refined_deg 1.088 r_angle_other_deg 0.799 r_mcangle_it 0.797 r_mcbond_it 0.401 r_mcbond_other 0.096 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4089 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction