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Conformational Closure of the Catalytic Site of Human CD38 Induced by Calcium
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 7.5 300 10% PEG 4000, 100mM MES, 100mM calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 1.83 32.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.687 α = 90 b = 60.058 β = 129.69 c = 56.932 γ = 90
Symmetry Space Group C 1 2 1
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 2006-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.978 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 1.45 30 91.5 0.044 0.044 25.28 3.3 39005 35690 1.4 2.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 1.5 52.6 0.326 2.08 1.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1YH3 1.45 20 36972 33844 1809 91.54 0.1482 0.1482 0.14624 0.1498 0.18416 0.1854 RANDOM 21.359
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] -0.06 -0.29 -0.18 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.449 r_dihedral_angle_4_deg 12.791 r_dihedral_angle_3_deg 11.382 r_dihedral_angle_1_deg 6.036 r_scangle_it 4.855 r_scbond_it 3.404 r_mcangle_it 2.431 r_mcbond_it 1.552 r_angle_refined_deg 1.326 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.449 r_dihedral_angle_4_deg 12.791 r_dihedral_angle_3_deg 11.382 r_dihedral_angle_1_deg 6.036 r_scangle_it 4.855 r_scbond_it 3.404 r_mcangle_it 2.431 r_mcbond_it 1.552 r_angle_refined_deg 1.326 r_nbtor_refined 0.313 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.091 r_symmetry_metal_ion_refined 0.05 r_metal_ion_refined 0.042 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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 1870 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 3
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling