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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Se-Met derived in-house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 17% (w/v) PEG 3350 and 0.18 M magnesium acetate
Crystal Properties Matthews coefficient Solvent content 2.94 58.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 243.374 α = 90 b = 49.778 β = 119.35 c = 135.746 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 PIXEL DECTRIS EIGER X 9M 2022-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9797 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 2.9 50 99.3 0.995 9.3 6.3 31976
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 2.9 2.95 0.581
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT in-house model 2.9 48.51 26461 1403 86.75 0.26699 0.26505 0.30408 0.2941 RANDOM 48.475
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] 0.28 0.07 0.17 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.597 r_long_range_B_other 10.548 r_long_range_B_refined 10.547 r_dihedral_angle_1_deg 7.948 r_mcangle_it 5.783 r_mcangle_other 5.783 r_scangle_other 5.18 r_mcbond_it 3.506 r_mcbond_other 3.505 r_scbond_it 3.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.597 r_long_range_B_other 10.548 r_long_range_B_refined 10.547 r_dihedral_angle_1_deg 7.948 r_mcangle_it 5.783 r_mcangle_other 5.783 r_scangle_other 5.18 r_mcbond_it 3.506 r_mcbond_other 3.505 r_scbond_it 3.189 r_scbond_other 3.189 r_dihedral_angle_2_deg 1.893 r_angle_refined_deg 1.102 r_angle_other_deg 0.725 r_chiral_restr 0.053 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 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 8586 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing