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Crystal structure of human CD38 in complex with compound CZ-27
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% PEG10000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.87 α = 109.56 b = 53.658 β = 90.95 c = 63.562 γ = 94.73
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 2010-03-31 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 1.65 50 95.9 0.071 14.4 3.9 59566
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 1.65 1.71 95.5 0.399 4 5944
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 1.65 50 59515 3006 95.34 0.1812 0.1798 0.209 0.2088 0.2393 RANDOM 33.447
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] -1.17 -0.02 0.11 0.41 0.61 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.864 r_dihedral_angle_4_deg 14.631 r_dihedral_angle_3_deg 12.826 r_dihedral_angle_1_deg 5.512 r_scangle_it 3.022 r_scbond_it 1.961 r_angle_refined_deg 1.282 r_mcangle_it 1.145 r_angle_other_deg 0.816 r_mcbond_it 0.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.864 r_dihedral_angle_4_deg 14.631 r_dihedral_angle_3_deg 12.826 r_dihedral_angle_1_deg 5.512 r_scangle_it 3.022 r_scbond_it 1.961 r_angle_refined_deg 1.282 r_mcangle_it 1.145 r_angle_other_deg 0.816 r_mcbond_it 0.574 r_mcbond_other 0.157 r_chiral_restr 0.138 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4082 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction