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Crystal structure of human CD38 extracellular domain E226Q mutant, NMN complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YH3 PDB ENTRY 1YH3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 298 100 mM MES pH 6.0, 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.858 α = 106.11 b = 53.228 β = 91.97 c = 65.67 γ = 95.03
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 ADSC QUANTUM 210 2006-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 30 97.5 0.09 0.09 21.2 3.8 41633 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.98 95.2 0.436 0.436 2.9 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1YH3 1.9 20 38959 38959 2061 100 0.188 0.185 0.2403 0.241 0.2824 RANDOM 33.29
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] -1.06 0.56 0.45 0.65 0.98 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.316 r_dihedral_angle_4_deg 17.826 r_dihedral_angle_3_deg 15.779 r_dihedral_angle_1_deg 6.39 r_scangle_it 4.537 r_scbond_it 2.975 r_mcangle_it 1.889 r_angle_refined_deg 1.772 r_mcbond_it 1.21 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.316 r_dihedral_angle_4_deg 17.826 r_dihedral_angle_3_deg 15.779 r_dihedral_angle_1_deg 6.39 r_scangle_it 4.537 r_scbond_it 2.975 r_mcangle_it 1.889 r_angle_refined_deg 1.772 r_mcbond_it 1.21 r_nbtor_refined 0.314 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.163 r_symmetry_vdw_refined 0.152 r_chiral_restr 0.129 r_symmetry_hbond_refined 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4010 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing