☰ Navigation Tabs
Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8K9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate.
10 mM NAD+ soaking
Crystal Properties Matthews coefficient Solvent content 2.38 48.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.222 α = 90 b = 48.931 β = 95.7 c = 178.603 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 9M 2022-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.000 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.35 29.62 99.8 0.999 11.6 6.9 98734
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 99.9 0.675
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 8K9Z 2.35 29.62 93729 4996 99.7 0.22 0.217 0.2228 0.263 0.2642 RANDOM 55.8
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] -1.31 -0.99 -0.38 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.662 r_long_range_B_refined 11.751 r_long_range_B_other 11.751 r_scangle_other 7.996 r_dihedral_angle_1_deg 7.508 r_mcangle_other 7.35 r_mcangle_it 7.349 r_scbond_it 5.049 r_scbond_other 5.049 r_mcbond_it 4.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.662 r_long_range_B_refined 11.751 r_long_range_B_other 11.751 r_scangle_other 7.996 r_dihedral_angle_1_deg 7.508 r_mcangle_other 7.35 r_mcangle_it 7.349 r_scbond_it 5.049 r_scbond_other 5.049 r_mcbond_it 4.814 r_mcbond_other 4.811 r_dihedral_angle_2_deg 4.668 r_angle_refined_deg 1.033 r_angle_other_deg 0.702 r_chiral_restr 0.049 r_bond_refined_d 0.011 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17526 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing