☰ Navigation Tabs
Crystal structure of human CD38 extracellular domain, 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 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.889 α = 106.2 b = 53.205 β = 91.84 c = 65.598 γ = 95.05
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 2006-05-01 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 1.8 30 96.7 0.099 0.099 12.6 3.4 47229 1.5
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) 1.8 1.86 87.2 0.443 0.443 1.5 2
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 1.81 20 44739 44739 2383 100 0.176 0.174 0.2626 0.217 0.2861 RANDOM 33.12
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] -0.71 0.16 0.15 0.32 0.6 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.719 r_dihedral_angle_4_deg 22.069 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 5.871 r_scangle_it 4.051 r_scbond_it 2.615 r_mcangle_it 1.56 r_angle_refined_deg 1.523 r_mcbond_it 0.98 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.719 r_dihedral_angle_4_deg 22.069 r_dihedral_angle_3_deg 15.886 r_dihedral_angle_1_deg 5.871 r_scangle_it 4.051 r_scbond_it 2.615 r_mcangle_it 1.56 r_angle_refined_deg 1.523 r_mcbond_it 0.98 r_nbtor_refined 0.312 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 4100 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing