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Crystal Structure of Human CD38 in Complex with 4'-Thioribose NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 100mM HEPES pH 7.0, 14-18% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.742 α = 90 b = 51.106 β = 96.89 c = 100.674 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M Mirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2018-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.395 99.948 99.9 0.368 0.368 0.392 0.133 0.961 6 8.7 23158
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99.9 1.468 1.561 0.525 0.736 1.3 8.7
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 1ZVM 2.4 30 21875 1176 99.67 0.2181 0.2157 0.2203 0.2618 0.2649 RANDOM 48.4
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] 4.09 -2.72 -3.04 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.152 r_dihedral_angle_3_deg 15.757 r_dihedral_angle_4_deg 15.503 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 1.42 r_angle_other_deg 0.987 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.152 r_dihedral_angle_3_deg 15.757 r_dihedral_angle_4_deg 15.503 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 1.42 r_angle_other_deg 0.987 r_chiral_restr 0.082 r_bond_refined_d 0.01 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 3893 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction