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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with UTP 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 0.2 M MOPS pH 6.5,
20% w/v Polyethylene glycol 4,000.
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.274 α = 101.137 b = 46.091 β = 106.903 c = 59.889 γ = 95.429
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) 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 1.984 30 96.4 0.997 25 6.6 23181
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 1.984 2.06 0.965
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 1.984 23.245 22117 1092 91.404 0.169 0.1667 0.1751 0.2092 0.2155 29.829
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] 0.034 -0.262 0.263 -0.418 -0.683 0.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.805 r_dihedral_angle_3_deg 15.019 r_dihedral_angle_4_deg 14.098 r_dihedral_angle_1_deg 6.738 r_lrange_it 6.116 r_lrange_other 6.074 r_scangle_it 4.739 r_scangle_other 4.737 r_mcangle_it 3.505 r_mcangle_other 3.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.805 r_dihedral_angle_3_deg 15.019 r_dihedral_angle_4_deg 14.098 r_dihedral_angle_1_deg 6.738 r_lrange_it 6.116 r_lrange_other 6.074 r_scangle_it 4.739 r_scangle_other 4.737 r_mcangle_it 3.505 r_mcangle_other 3.504 r_scbond_it 3.053 r_scbond_other 3.052 r_mcbond_it 2.416 r_mcbond_other 2.415 r_angle_refined_deg 1.352 r_angle_other_deg 1.291 r_nbd_other 0.209 r_nbd_refined 0.196 r_symmetry_nbd_refined 0.188 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2647 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling