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Dynamic conformations of the CD38-mediated NAD cyclization captured using multi-copy crystallography
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 4 298 0.1M sodium acetate pH 4.0, 15% PEG 4000, 0.2M ammonium acetate, 3% isopropanol, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.655 α = 90 b = 146.662 β = 90 c = 191.086 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-225 2009-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97623 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 100 97.7 0.095 12.6 7.1 79445
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) 2.2 2.28 89.9 0.354 4.6 7208
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 PDB ENTRY 1YH3 2.2 48.73 79380 3969 97.25 0.2057 0.2033 0.2233 0.2496 0.2642 RANDOM 47.9
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] 0.59 1.99 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.476 r_dihedral_angle_4_deg 15.11 r_dihedral_angle_3_deg 13.316 r_dihedral_angle_1_deg 5.501 r_scangle_it 2.346 r_scbond_it 1.489 r_angle_refined_deg 1.17 r_mcangle_it 0.861 r_angle_other_deg 0.822 r_mcbond_it 0.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.476 r_dihedral_angle_4_deg 15.11 r_dihedral_angle_3_deg 13.316 r_dihedral_angle_1_deg 5.501 r_scangle_it 2.346 r_scbond_it 1.489 r_angle_refined_deg 1.17 r_mcangle_it 0.861 r_angle_other_deg 0.822 r_mcbond_it 0.445 r_mcbond_other 0.095 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11346 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 210
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction