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Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with UTP
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 2.34 47.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.375 α = 101.796 b = 46.302 β = 106.802 c = 60.792 γ = 95.768
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 9M 2021-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.897 30 94.7 0.038 21.865 2.4 26575
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 1.897 1.97 0.983
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 1.897 23.452 26517 1320 93.975 0.177 0.1752 0.1851 0.207 0.2136 24.106
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] 0.095 -0.015 0.146 -0.18 -0.301 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.389 r_dihedral_angle_4_deg 16.556 r_dihedral_angle_3_deg 14.466 r_dihedral_angle_1_deg 6.731 r_lrange_it 6.547 r_lrange_other 6.466 r_scangle_it 4.859 r_scangle_other 4.858 r_mcangle_it 3.371 r_mcangle_other 3.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.389 r_dihedral_angle_4_deg 16.556 r_dihedral_angle_3_deg 14.466 r_dihedral_angle_1_deg 6.731 r_lrange_it 6.547 r_lrange_other 6.466 r_scangle_it 4.859 r_scangle_other 4.858 r_mcangle_it 3.371 r_mcangle_other 3.371 r_scbond_it 3.137 r_scbond_other 3.136 r_mcbond_it 2.314 r_mcbond_other 2.314 r_angle_refined_deg 1.425 r_angle_other_deg 1.308 r_nbd_other 0.207 r_nbd_refined 0.206 r_symmetry_nbd_other 0.188 r_symmetry_xyhbond_nbd_refined 0.187 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.166 r_symmetry_nbd_refined 0.157 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2616 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling