☰ Navigation Tabs
Crystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 22% (w/v) PEG 3350 and 4% (v/v) Tacsimate (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 3.58 65.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.726 α = 90 b = 207.726 β = 90 c = 54.647 γ = 120
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 2022-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9795 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 3.38 50 99.6 0.996 11.1 6.2 17817
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 3.38 3.44 0.568
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 3.38 40.42 15125 830 82.79 0.28789 0.28599 0.2844 0.32212 0.3167 RANDOM 54.37
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] 0.37 0.18 0.37 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.601 r_dihedral_angle_4_deg 25.585 r_dihedral_angle_3_deg 23.171 r_long_range_B_refined 10.794 r_long_range_B_other 10.793 r_dihedral_angle_1_deg 6.991 r_mcangle_it 6.279 r_mcangle_other 6.279 r_scangle_other 5.102 r_mcbond_it 3.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.601 r_dihedral_angle_4_deg 25.585 r_dihedral_angle_3_deg 23.171 r_long_range_B_refined 10.794 r_long_range_B_other 10.793 r_dihedral_angle_1_deg 6.991 r_mcangle_it 6.279 r_mcangle_other 6.279 r_scangle_other 5.102 r_mcbond_it 3.622 r_mcbond_other 3.616 r_scbond_it 2.868 r_scbond_other 2.868 r_angle_other_deg 2.328 r_angle_refined_deg 1.312 r_chiral_restr 0.079 r_bond_other_d 0.035 r_gen_planes_refined 0.012 r_gen_planes_other 0.012 r_bond_refined_d 0.009 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 5848 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing