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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with CTP Mn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other apo DwCdnB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M BIS-TRIS propane pH 9.0,
30% w/v Polyethylene glycol 6,000.
Crystal Properties Matthews coefficient Solvent content 2.47 50.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.401 α = 105.45 b = 46.765 β = 103.349 c = 64.182 γ = 99.327
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 EIGER2 X 16M 2022-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97626 NSRRC TPS 07A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 30 96.7 0.044 1 40.4 6.8 57942
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 1.5 1.55 0.978
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.5 23.508 57636 2791 96.001 0.174 0.1734 0.1737 0.1927 0.1927 19.78
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] -0.015 -0.033 0.042 -0.021 -0.152 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.48 r_dihedral_angle_4_deg 13.974 r_dihedral_angle_3_deg 13.074 r_dihedral_angle_1_deg 6.528 r_lrange_it 5.975 r_lrange_other 5.799 r_scangle_it 4.453 r_scangle_other 4.432 r_mcangle_it 3.211 r_mcangle_other 3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.48 r_dihedral_angle_4_deg 13.974 r_dihedral_angle_3_deg 13.074 r_dihedral_angle_1_deg 6.528 r_lrange_it 5.975 r_lrange_other 5.799 r_scangle_it 4.453 r_scangle_other 4.432 r_mcangle_it 3.211 r_mcangle_other 3.21 r_scbond_it 2.88 r_scbond_other 2.864 r_mcbond_it 2.142 r_mcbond_other 2.142 r_angle_refined_deg 1.445 r_angle_other_deg 1.408 r_nbd_other 0.29 r_nbd_refined 0.214 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.185 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.171 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.08 r_xyhbond_nbd_other 0.041 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2647 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling