☰ Navigation Tabs
Structural Basis for the Mechanistic Understanding Human CD38 Controlled Multiple Catalysis
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 VAPOR DIFFUSION, HANGING DROP 6.5 298 100 mM MES, 12% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.893 α = 109.36 b = 51.152 β = 91.22 c = 65.639 γ = 97.38
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 2005-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.976 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 50 94.9 54974 52170 3.3 3.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 71.8
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1YH3 1.71 20 52418 49477 2665 94.39 0.195 0.19129 0.1889 0.23614 0.2997 RANDOM 33.576
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] -0.8 0.46 0.52 0.96 0.97 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_4_deg 20.094 r_dihedral_angle_3_deg 16.303 r_dihedral_angle_1_deg 5.997 r_scangle_it 3.902 r_scbond_it 2.725 r_mcangle_it 1.691 r_angle_refined_deg 1.626 r_mcbond_it 1.039 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_4_deg 20.094 r_dihedral_angle_3_deg 16.303 r_dihedral_angle_1_deg 5.997 r_scangle_it 3.902 r_scbond_it 2.725 r_mcangle_it 1.691 r_angle_refined_deg 1.626 r_mcbond_it 1.039 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.203 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.112 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 3995 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing