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X-ray structure of human CD38 catalytic domain with 2'-Cl-araNAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 1) 100mM HEPES pH 7.0, 2) 38-42% Morpheus Precipitant mix 1 (MD2-250-84) containing PEG 1K, 3350 and MPD, 3) 100mM Potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.762 α = 90 b = 114.762 β = 90 c = 97.154 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 114.762 100 0.088 0.091 0.02 0.999 16.2 19.8 103758 23.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 100 1.75 1.75 1.801 0.42 0.748 0.4 18.1
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 6EDR 1.5 28.71 98376 5329 99.97 0.1676 0.1664 0.1725 0.1902 0.1944 RANDOM 30.512
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] -0.98 -0.98 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.562 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_1_deg 6.321 r_angle_refined_deg 1.84 r_angle_other_deg 1.519 r_chiral_restr 0.35 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.562 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_1_deg 6.321 r_angle_refined_deg 1.84 r_angle_other_deg 1.519 r_chiral_restr 0.35 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4044 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 151
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction